Cell-permeable (CP)-Δ SOCS3 recombinant protein and uses thereof

ABSTRACT

The present invention is related to development of the improved cell-permeable (CP)-ΔSOCS3 recombinant protein which disrupt the interaction of leptin receptor (ObR) and suppressor of cytokine signaling 3 (SOCS3), as protein-based anti-obesity or anti-diabetes agent by utilizing the platform technology for macromolecule intracellular transduction.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a Bypass Continuation of International Application No. PCT/KR2016/008831 filed Aug. 11, 2016, which claims benefit from U.S. provisional application No. 62/206,587 filed Aug. 18, 2015, contents of which are incorporated herein by reference in their entirety.

TECHNICAL FIELD

The present invention relates to development of the improved cell-permeable (CP)-truncated SOCS3 (ΔSOCS3) recombinant protein which disrupts the interaction of leptin receptor (ObR) and suppressor of cytokine signaling 3 (SOCS3), as protein-based anti-obesity or anti-diabetes agent by utilizing the platform technology for macromolecule intracellular transduction.

BACKGROUND ART

The global prevalence of obesity has increased dramatically worldwide including Korea over the last decades and has now reached epidemic proportions (16). According to the World Health Organization, 35% of adults worldwide aged >20 years were overweight (34% men and 35% women) in 2008.

Obesity is a metabolic disease and characterized as the accumulation of excessive body fat by hypertrophy and hyperplasia of adipocytes (17). Many factors that can cause obesity include an intake of high calorice meals, genetic defects, disorders of hormonale secretions and a lack of activity. Obesity is involved in the onset of various diseases, including coronary heart disease, hypertension type II diabetes, stroke, gallbladder disease, and osteoarthritis (18-22).

Adipose tissue is an endocrine organ that secretes adipokines to regulate nutrient homeostasis (23, 24). Leptin is an adipokine and a multi-functional cytokine. It is an endocrine hormone and suppresses appetite. It induces the expression of proopiomelanocortin (POMC) via binding to leptin receptor expressed on the neuronal cells in the hypothalamus. Serum leptin levels are regulated by fat mass, if weight is reduced, concentration of leptin is decreased that increases appetites and decreases energy expenditure. Reversely, increased fat more secrets leptin which reduces appetites. Adipose tissue-released leptin binds to the leptin receptor (ObR) which is expressed on the surface of neuronal cells through the blood-brain barrier (BBB). ObR is expressed most cells and contains extracellular domain including leptin binding site and intracellular domain associated with janus kinase2 (JAK2). Several signal transducers and activators of transcriptions (STATs) including STAT1, STATS, and STATS can bind to ObR. In addition, Src homology 2 domain-containing tyrosine phosphatase 2 (SHP2) also binds to ObR. When leptin binds to ObR, JAK2 is activated and phosphorylated. The activated JAK2 phosphorylates tyrosine residues positioned at 985, 1077, 1138 on ObR and recruits and phosphorylates down-stream signaling molecules. Phosphorylated STATs are dimerized and translocated from cytosol to the nucleus and induces the expression of target genes. This signaling ultimately decreases food intake and weight loss (25-27). Previously, leptin was developed as anti-obesity drug but this trial was failed due to existence of leptin resistance in obese humans. In the obese environment, serum leptin levels increase, and promote leptin resistance that leads to more severe obesity (28). Leptin resistance has been the main reason behind the unsuccessful application of leptin as an anti-obesity agent. Leptin signaling induces the expression of suppressor of cytokine signaling 3 (SOCS3), which is an endogenous negative feedback inhibitor (29-31). SOCS3 binds to an intracellular domain of ObR via SH2 domain and suppresses leptin signaling through inhibition of JAK activity and degradation of ObR. According to the previous studies, neuronal deletion of SOCS3 prevented leptin resistance in animal on high fat diet (32, 33).

REFERENCES

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DISCLOSURE Technical Problem

Various problems including poor penetration into a cell and tissue and/or low solubility and yield have restricted the usage of macromolecules including cargo protein, as a novel medical drug.

Technical Solution

To resolve these problems, newly designed advanced macromolecule transduction domain (aMTD)-enabled macromolecule intracellular transduction technology (MITT) has been adopted for the development of novel protein therapy using truncated SOCS3 against obesity and diabetes.

For MITT, six critical factors (length, bending potential, instability index, aliphatic index, GRAVY, amino acid composition) have been determined through analysis of baseline hydrophobic CPPs. Advanced macromolecule transduction domain (aMTD), newly designed based on these six critical factors, could optimize cell-/tissue-permeability of cargo proteins that have a therapeutic effects and develop them as protein-based drugs. Further, in order to increase solubility and yield of recombinant protein, solubilization domains (SDs) additionally fused to the aMTD-cargo recombinant protein, thereby notably increased the solubility and yield of the recombinant protein.

One aspect disclosed in the present application provides a cell-permeable (CP)-truncated SOCS3 (ΔSOCS3) recombinant protein that contains the SH2 domain of SOCS3, with the advanced macromolecule transduction domains (aMTD) to inhibit the interaction between ObR and SOCS3 in a competitive manner to control the leptin resistance. The CP-ΔSOCS3 recombinant protein has high solubility, manufacturing yield and efficiency of membrane penetrating ability both in vitro and in vivo.

The present inventors have hypothesized that the CP-ΔSOCS3 recombinant protein is capable of competitively disrupt interactions between ObR (leptin receptor) and SOCS3 (Suppressor of cytokine signaling 3) which major reason of leptin resistance. To prove said hypothesis, CP-ΔSOCS3 comprising a truncated form of SOCS3 containing only SH2 (Src homology 2) domain of SOCS3; and novel hydrophobic CPP (Cell-Permeable Peptide)—aMTD being fused to the truncated form of SOCS3 have been developed. This recombinant protein would have much improved physicochemical characteristics (solubility and yield) and functional activity (cell-/tissue-permeability) that are capable of competitively disrupt the interactions between ObR and SOCS3. The therapeutic applicability of CP-ΔSOCS3 as anti-obesity drug that helps to maintain the leptin-induced anti-appetite signals and to return to normal appetite regulations by competitive inhibition of SOCS3 was also proved in the present disclosure.

One aspect disclosed in the present application provides an Cell-Permeable (CP)-ΔSOCS3 recombinant protein, which comprises a ΔSOCS3 protein containing SH2 domain of SOCS3 protein; and an advanced macromolecule transduction domain (aMTD) being composed of 9-13 amino acid sequences and having improved cell or tissue permeability, wherein the aMTD is fused to one end or both ends of the ΔSOCS3 protein and has the following features of:

(a) being composed of 3 or more amino acid sequences selected from the group consisting of Ala, Val, Ile, Leu, and Pro;

(b) having proline as amino acid sequences corresponding to any one or more of positions 5 to 8, and 12 of its amino acid sequence; and

(c) having an instability index of 40-60; an aliphatic index of 180-220; and a grand average of hydropathy (GRAVY) of 2.1-2.6, as measured by Protparam.

According to one embodiment, one or more solubilization domain (SD)(s) are further fused to the end(s) of one or more of the ΔSOCS3 protein and the aMTD.

According to another embodiment, the aMTD may have α-Helix structure. According to still another embodiment, the aMTD may be composed of 12 amino acid sequences and represented by the following general formula:

wherein X(s) independently refer to Alanine (A), Valine (V), Leucine (L) or Isoleucine (I); and Proline (P) can be positioned in one of U(s) (either 5′, 6′, 7′ or 8′). The remaining U(s) are independently composed of A, V, L or I, P at the 12′ is Proline.

Another aspect disclosed in the present application provides a CP-ΔSOCS3 recombinant protein which is represented by any one of the following structural formulae: A-B-C, A-C-B, B-A-C, B-C-A, C-A-B, C-B-A and A-C-B-C

wherein A is an advanced macromolecule transduction domain (aMTD) having improved cell or tissue permeability, B is a ΔSOCS3 protein containing a SH2 domain of SOCS3 protein, and C is a solubilization domain (SD); and

the aMTD is composed of 9-13 amino acid sequences and has the following features of:

(a) being composed of 3 or more amino acids selected from the group consisting of Ala, Val, Ile, Leu, and Pro;

(b) having proline as amino acid sequences corresponding to any one or more of positions 5 to 8, and 12 of its amino acid sequence;

(c) having an instability index of 40-60; an aliphatic index of 180-220; and a grand average of hydropathy (GRAVY) of 2.1-2.6, as measured by Protparam; and

(d) having α-Helix structure.

According to one embodiment disclosed in the present application, the ΔSOCS3 protein may have an amino acid sequence of SEQ ID NO: 816.

According to another embodiment disclosed in the present application, the ΔSOCS3 protein may be encoded by a polynucleotide sequence of SEQ ID NO: 817.

According to still another embodiment disclosed in the present application, the ΔSOCS3 protein may further include a ligand selectively binding to a receptor of a cell, a tissue, or an organ.

According to still another embodiment disclosed in the present application, the aMTD may have an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-240 and 822.

According to still another embodiment disclosed in the present application, the aMTD may be encoded by a polynucleotide sequence selected from the group consisting of SEQ ID NOs: 241-480 and 823.

According to still another embodiment disclosed in the present application, the SD(s) may have an amino acid sequence independently selected from the group consisting of SEQ ID NOs: 798, 799, 800, 801, 802, 803, and 804.

According to still another embodiment disclosed in the present application, the SD(s) may be encoded by a polynucleotide sequence independently selected from the group consisting of SEQ ID NOs: 805, 806, 807, 808, 809, 810, and 811.

According to still another embodiment disclosed in the present application, the CP-ΔSOCS3 recombinant protein may have a histidine-tag affinity domain additionally fused to one end thereof.

According to still another embodiment disclosed in the present application, the histidine-tag affinity domain may have an amino acid sequence of SEQ ID NO: 812.

According to still another embodiment disclosed in the present application, the histidine-tag affinity domain may be encoded by a polynucleotide sequence of SEQ ID NO: 813.

According to still another embodiment disclosed in the present application, the fusion may be formed via a peptide bond or a chemical bond.

According to still another embodiment disclosed in the present application, the CP-ΔSOCS3 recombinant protein may be used for the treatment or prevention of obesity or diabetes.

Still another aspect disclosed in the present application provides a polynucleotide sequence encoding the CP-ΔSOCS3 recombinant protein.

According to one embodiment disclosed in the present application, the polynucleotide sequence may be a polynucleotide sequence represented by SEQ ID NO: 819.

According to another embodiment disclosed in the present application, the polynucleotide sequence may be a polynucleotide sequence represented by SEQ ID NOs: 821.

Still another aspect disclosed in the present application provides a recombinant expression vector including the polynucleotide sequence.

Still another aspect disclosed in the present application provides a transformant transformed with the recombinant expression vector.

Still another aspect disclosed in the present application provides a preparing method of the CP-ΔSOCS3 recombinant protein including preparing the recombinant expression vector; preparing the transformant using the recombinant expression vector; culturing the transformant; and recovering the recombinant protein expressed by the culturing.

Still another aspect disclosed in the present application provides a composition including the CP-ΔSOCS3 recombinant protein as an active ingredient.

Still another aspect disclosed in the present application provides a pharmaceutical composition for treating or preventing obesity or diabetes including the CP-ΔSOCS3 recombinant protein as an active ingredient; and a pharmaceutically acceptable carrier.

Still another aspect disclosed in the present application provides use of the CP-ΔSOCS3 recombinant protein as a medicament for treating or preventing obesity or diabetes.

Still another aspect disclosed in the present application provides a medicament including the CP-ΔSOCS3 recombinant protein.

Still another aspect disclosed in the present application provides use of the CP-ΔSOCS3 recombinant protein in the preparation of a medicament for treating or preventing obesity or diabetes.

Still another aspect disclosed in the present application provides a method of treating or preventing obesity or diabetes in a subject, the method including identifying a subject in need of treatment or prevention of obesity or diabetes; and administering to the subject a therapeutically effective amount of the CP-ΔSOCS3 recombinant protein.

According to one embodiment disclosed in the present application, the subject may be a mammal.

Unless defined otherwise, all terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the present invention belongs. Although a certain method and a material is described herein, it should not be construed as being limited thereto, any similar or equivalent method and material to those may also be used in the practice or testing of the present invention. All publications mentioned herein are incorporated herein by reference in their entirety to disclose and describe the methods and/or materials in connection with which the publications are cited. It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise.

A “peptide,” as used herein, refers to a chain-type polymer formed by amino acid residues which are linked to each other via peptide bonds, and used interchangeably with “polypeptide.” Further, a “polypeptide” includes a peptide and a protein.

Further, the term “peptide” includes amino acid sequences that are conservative variations of those peptides specifically exemplified herein. The term “conservative variation,” as used herein, denotes the replacement of an amino acid residue by another, biologically similar residue. Examples of conservative variations include substitution of one hydrophobic residue, such as isoleucine, valine, leucine, alanine, cysteine, glycine, phenylalanine, proline, tryptophan, tyrosine, norleucine, or methionine for another, or substitution of one polar residue for another, for example, substitution of arginine for lysine, glutamic acid for aspartic acid, or glutamine for asparagine, and the like. Neutral hydrophilic amino acids which may be substituted for one another include asparagine, glutamine, serine, and threonine.

The term “conservative variation” also includes use of a substituted amino acid in place of an unsubstituted parent amino acid, provided that antibodies raised to the substituted polypeptide also immunoreact with the unsubstituted polypeptide. Such conservative substitutions are within the definition of the classes of the peptides disclosed in the present application.

A person having ordinary skill in the art may make similar substitutions to obtain peptides having higher cell permeability and a broader host range. For example, one aspect disclosed in the present application provides peptides corresponding to amino acid sequences (e.g. SEQ ID NOs: 1 to 240 and 822) provided herein, as well as analogues, homologs, isomers, derivatives, amidated variations, and conservative variations thereof, as long as the cell permeability of the peptide remains.

Minor modifications to primary amino acid sequence disclosed in the present application may result in peptides which have substantially equivalent or enhanced cell permeability, as compared to the specific peptides described herein. Such modifications may be deliberate, as by site-directed mutagenesis, or may be spontaneous.

All peptides may be synthesized using L-amino acids, but D forms of all of the peptides may be synthetically produced. In addition, C-terminal derivatives, such as C-terminal methyl esters and C-terminal amidates, may be produced in order to increase the cell permeability of the peptide according to one embodiment disclosed in the present application.

All of the peptides produced by these modifications are included herein, as long as in the case of amidated versions of the peptide, the cell permeability of the original peptide is altered or enhanced such that the amidated peptide is therapeutically useful. It is envisioned that such modifications are useful for altering or enhancing cell permeability of a particular peptide.

Furthermore, deletion of one or more amino acids may also result in a modification to the structure of the resultant molecule without any significant change in its cell permeability. This may lead to the development of a smaller active molecule which may also have utility. For example, amino- or carboxyl-terminal amino acids which may not be required for the cell permeability of a particular peptide may be removed.

The term “gene” refers to an arbitrary nucleic acid sequence or a part thereof having a functional role in protein coding or transcription, or regulation of other gene expression. The gene may be composed of all nucleic acids encoding a functional protein or a part of the nucleic acid encoding or expressing the protein. The nucleic acid sequence may include a gene mutation in exon, intron, initiation or termination region, promoter sequence, other regulatory sequence, or a unique sequence adjacent to the gene.

The term “primer” refers to an oligonucleotide sequence that hybridizes to a complementary RNA or DNA target polynucleotide and serves as the starting points for the stepwise synthesis of a polynucleotide from mononucleotides by the action of a nucleotidyltransferase as occurs, for example, in a polymerase chain reaction.

The term “coding region” or “coding sequence” refers to a nucleic acid sequence, a complement thereof, or a part thereof which encodes a particular gene product or a fragment thereof for which expression is desired, according to the normal base pairing and codon usage relationships. Coding sequences include exons in genomic DNA or immature primary RNA transcripts, which are joined together by the cellular biochemical machinery to provide a mature mRNA. The anti-sense strand is the complement of the nucleic acid, and the coding sequence may be deduced therefrom.

One aspect disclosed in the present application provides an CP-ΔSOCS3 recombinant protein, which comprises a ΔSOCS3 protein containing a SH2 domain of SOCS3 protein; and an advanced macromolecule transduction domain (aMTD) being composed of 9-13 amino acid sequences, preferably 10-12 amino acid sequences, and having improved cell or tissue permeability, wherein the aMTD is fused to one end or both ends of the ΔSOCS3 protein and has the following features of:

(a) being preferably composed of 3 or more amino acid sequences selected from the group consisting of Ala, Val, Ile, Leu, and Pro;

(b) having proline as amino acid sequences corresponding to any one or more of positions 5 to 8, and 12 of its amino acid sequence, and preferably one or more of positions 5 to 8 and position 12 of its amino acid sequence; and

(c) having an instability index of preferably 40-60 and more preferably 41-58; an aliphatic index of preferably 180-220 and more preferably 185-225; and a grand average of hydropathy (GRAVY) of preferably 2.1-2.6 and more preferably 2.2-2.6 as measured by Protparam (see http://web.expasy.org/protparam/).

These critical factors that facilitate the cell permeable ability of aMTD sequences were analyzed, identified, and determined according to one embodiment disclosed in the present application. These aMTD sequences are artificially assembled based on the critical factors (CFs) determined from in-depth analysis of previously published hydrophobic CPPs.

The aMTD sequences according to one aspect disclosed in the present application are the first artificially developed cell permeable polypeptides capable of mediating the transduction of biologically active macromolecules—including peptides, polypeptides, protein domains, or full-length proteins—through the plasma membrane of cells.

According to one embodiment, one or more solubilization domain (SD)(s) are further fused to one or more of the ΔSOCS3 protein and the aMTD, preferably one end or both ends of the ΔSOCS3 protein, and more preferably the C-terminus of the ΔSOCS3 protein.

According to another embodiment, the aMTD may have α-Helix structure.

According to still another embodiment, the aMTD may be preferably composed of 12 amino acid sequences and represented by the following general formula:

Here, X(s) independently refer to Alanine (A), Valine (V), Leucine (L) or Isoleucine (I); and Proline (P) can be positioned in one of U(s) (either 5′, 6′, 7′ or 8′). The remaining U(s) are independently composed of A, V, L or I, P at the 12′ is Proline.

Still another aspect disclosed in the present application provides a CP-ΔSOCS3 recombinant protein which is represented by any one of structural formulae A-B-C, A-C-B, B-A-C, B-C-A, C-A-B, C-B-A and A-C-B-C, and preferably by A-B-C or C-B-A:

wherein A is an advanced macromolecule transduction domain (aMTD) having improved cell or tissue permeability, B is a ΔSOCS3 protein containing a SH2 domain of SOCS3 protein, and C is a solubilization domain (SD); and

the aMTD is composed of 9-13, preferably 10-12 amino acid sequences and has the following features of:

(a) being composed of 3 or more amino acid sequences selected from the group consisting of Ala, Val, Ile, Leu, and Pro;

(b) having proline as amino acid sequences corresponding to any one or more of positions 5 to 8, and 12 of its amino acid sequence, and preferably, one or more of positions 5 to 8 and position 12 of its amino acid sequence;

(c) having an instability index of 40-60, preferably 41-58 and more preferably 50-58; an aliphatic index of 180-220. preferably 185-225 and more preferably 195-205; and a grand average of hydropathy (GRAVY) of 2.1-2.6 and preferably 2.2-2.6, as measured by Protparam (see http://web.expasy.org/protparam/); and

(d) preferably having α-Helix structure.

In one embodiment disclosed in the present application, the ΔSOCS3 protein may have an amino acid sequence of SEQ ID NO: 816.

In another embodiment disclosed in the present application, the ΔSOCS3 protein may be encoded by a polynucleotide sequence of SEQ ID NO: 817.

When the CP-ΔSOCS3 recombinant protein is intended to be delivered to a particular cell, tissue, or organ, the ΔSOCS3 protein may form a fusion product, together with an extracellular domain of a ligand capable of selectively binding to a receptor which is specifically expressed on the particular cell, tissue, or organ, or monoclonal antibody (mAb) capable of specifically binding to the receptor or the ligand and a modified form thereof.

The binding of the peptide and a biologically active substance may be formed either by indirect linkage by a cloning technique using an expression vector at a nucleotide level or by direct linkage via chemical or physical covalent or non-covalent bond of the peptide and the biologically active substance.

In still another embodiment disclosed in the present application, the ΔSOCS3 protein may preferably further include a ligand selectively binding to a receptor of a cell, a tissue, or an organ.

In one embodiment disclosed in the present application, the aMTD may have an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-240 and 822, preferably SEQ ID NOs: 2, 12, 34, 39, 82, 91, 98, 105, 107, 121, 125, 130, 131, 143, 147, 177, 222, 228, 229 and 822, more preferably SEQ ID NOs: 12 and 121.

In still another embodiment disclosed in the present application, the aMTD may be encoded by a polynucleotide sequence selected from the group consisting of SEQ ID NOs: 241-480 and 823, preferably SEQ ID NOs: 242, 252, 274, 279, 322, 331, 338, 345, 347, 361, 365, 370, 371, 383, 387, 417, 462, 468, 469 and 823, more preferably SEQ ID NO: 252 and 361.

In still another embodiment disclosed in the present application, the SD(s) may have an amino acid sequence independently selected from the group consisting of SEQ ID NOs: 798, 799, 800, 801, 802, 803, and 804. The SD may be preferably SDA of SEQ ID NO: 798, SDB of SEQ ID NO: 799, or SDB′ of SEQ ID NO: 804, and more preferably, SDB of SEQ ID NO: 799 which has superior structural stability, or SDB′ of SEQ ID NO: 804 which has a modified amino acid sequence of SDB to avoid immune responses upon in vivo application. The modification of the amino acid sequence in SDB may be replacement of an amino acid residue, Valine, corresponding to position 28 of the amino acid sequence of SDB (SEQ ID NO: 799) by Leucine.

In still another embodiment disclosed in the present application, the SDs may be encoded by a polynucleotide sequence independently selected from the group consisting of SEQ ID NOs: 805, 806, 807, 808, 809, 810, and 811. The SD may be preferably SDA encoded by a polynucleotide sequence of SEQ ID NO: 805, SDB encoded by a polynucleotide sequence of SEQ ID NO: 806, or SDB′ for deimmunization (or humanization) encoded by a polynucleotide sequence of SEQ ID NO: 811, and more preferably, SDB having superior structural stability, which is encoded by a polynucleotide sequence of SEQ ID NO: 806, or SDB′ having a modified polynucleotide sequence of SDB to avoid immune responses upon in vivo application, which is encoded by a polynucleotide sequence of SEQ ID NO: 811.

In still another embodiment disclosed in the present application, the CP-ΔSOCS3 recombinant protein may be preferably selected from the group consisting of:

1) a recombinant protein, in which ΔSOCS3 having an amino acid sequence of SEQ ID NO: 816 is fused to the N-terminus or the C-terminus of aMTD having any one amino acid sequence selected from the group consisting of SEQ ID NOs: 1 to 240 and 822, preferably SEQ ID NOs: 2, 12, 34, 39, 82, 91, 98, 105, 107, 121, 125, 130, 131, 143, 147, 177, 222, 228, 229 and 822, and more preferably SEQ ID NOs: 12 and 121;

2) a recombinant protein, in which SD having any one amino acid sequence selected from the group consisting of SEQ ID NOs: 798 to 804 is further fused to one or more of the N-terminus or the C-terminus of the ΔSOCS3 and aMTD in the recombinant protein of 1); and

3) a recombinant protein, in which a Histidine tag having an amino acid sequence of 812 is further fused to the N-terminus of the recombinant protein of 1) or 2).

Preferably, the CP-ΔSOCS3 recombinant protein may be composed of an amino acid sequence selected from the group consisting of SEQ ID NOs: 818 and 820.

The ΔSOCS3 protein may exhibit a physiological phenomenon-related activity or a therapeutic purpose-related activity by intracellular or in-vivo delivery. The recombinant expression vector may include a tag sequence which makes it easy to purify the recombinant protein, for example, consecutive histidine codon, maltose binding protein codon, Myc codon, etc., and further include a fusion partner to enhance solubility of the recombinant protein, etc. Further, for the overall structural and functional stability of the recombinant protein or flexibility of the proteins encoded by respective genes, the recombinant expression vector may further include one or more glycine, proline, and spacer amino acid or polynucleotide sequences including AAY amino acids. Furthermore, the recombinant expression vector may include a sequence specifically digested by an enzyme in order to remove an unnecessary region of the recombinant protein, an expression regulatory sequence, and a marker or reporter gene sequence to verify intracellular delivery, but is not limited thereto.

In still another embodiment disclosed in the present application, the CP-ΔSOCS3 recombinant protein may preferably have a histidine-tag affinity domain additionally fused to one end thereof.

In still another embodiment disclosed in the present application, the histidine-tag affinity domain may have an amino acid sequence of SEQ ID NO: 812.

In still another embodiment disclosed in the present application, the histidine-tag affinity domain may be encoded by a polynucleotide sequence of SEQ ID NO: 813.

In still another embodiment disclosed in the present application, the fusion may be formed via a peptide bond or a chemical bond.

The chemical bond may be preferably selected from the group consisting of disulfide bonds, diamine bonds, sulfide-amine bonds, carboxyl-amine bonds, ester bonds, and covalent bonds.

In still another embodiment disclosed in the present application, the CP-ΔSOCS3 recombinant protein may be used for the treatment or prevention of obesity or diabetes.

Still another aspect disclosed in the present application provides a polynucleotide sequence encoding the CP-ΔSOCS3.

According to still another embodiment disclosed in the present application, the polynucleotide sequence may be fused with a histidine-tag affinity domain.

Still another aspect disclosed in the present application provides a recombinant expression vector including the polynucleotide sequence.

Preferably, the vector may be inserted in a host cell and recombined with the host cell genome, or refers to any nucleic acid including a nucleotide sequence competent to replicate spontaneously as an episome. Such a vector may include a linear nucleic acid, a plasmid, a phagemid, a cosmid, an RNA vector, a viral vector, etc.

Preferably, the vector may be genetically engineered to incorporate the nucleic acid sequence encoding the recombinant protein in an orientation either N-terminal and/or C-terminal to a nucleic acid sequence encoding a peptide, a polypeptide, a protein domain, or a full-length protein of interest, and in the correct reading frame so that the recombinant protein consisting of aMTD, ΔSOCS3 protein, and preferably SD may be expressed. Expression vectors may be selected from those readily available for use in prokaryotic or eukaryotic expression systems.

Standard recombinant nucleic acid methods may be used to express a genetically engineered recombinant protein. The nucleic acid sequence encoding the recombinant protein according to one embodiment disclosed in the present application may be cloned into a nucleic acid expression vector, e.g., with appropriate signal and processing sequences and regulatory sequences for transcription and translation, and the protein may be synthesized using automated organic synthetic methods. Synthetic methods of producing proteins are described in, for example, the literature [Methods in Enzymology, Volume 289: Solid-Phase Peptide Synthesis by Gregg B. Fields (Editor), Sidney P. Colowick, Melvin I. Simon (Editor), Academic Press (1997)].

In order to obtain high level expression of a cloned gene or nucleic acid, for example, a cDNA encoding the recombinant protein according to one embodiment disclosed in the present application, the recombinant protein sequence may be typically subcloned into an expression vector that includes a strong promoter for directing transcription, a transcription/translation terminator, and in the case of a nucleic acid encoding a protein, a ribosome binding site for translational initiation. Suitable bacterial promoters are well known in the art and are described, e.g., in the literatures [Sambrook & Russell, Molecular Cloning: A Laboratory Manual, 3d Edition, Cold Spring Harbor Laboratory, N.Y. (2001); and Ausubel, et al., Current Protocols in Molecular Biology, Greene Publishing Associates and Wiley Interscience, N.Y. (1989)]. Bacterial expression systems for expression of the recombinant protein are available in, e.g., E. coli, Bacillus sp., and Salmonella (Palva et al., Gene 22: 229-235 (1983); Mosbach et al., Nature 302: 543-545 (1983)). Kits for such expression systems are commercially available. Eukaryotic expression systems for mammalian cells, yeast, and insect cells are well known in the art and are also commercially available. The eukaryotic expression vector may be preferably an adenoviral vector, an adeno-associated vector, or a retroviral vector.

Generally, the expression vector for expressing the cell permeable recombinant protein according to one embodiment disclosed in the present application in which the cargo protein, i.e. ΔSOCS3 protein, is attached to the N-terminus, C-terminus, or both termini of aMTD may include regulatory sequences including, for example, a promoter, operably attached to a sequence encoding the advanced macromolecule transduction domain. Non-limiting examples of inducible promoters that may be used include steroid-hormone responsive promoters (e.g., ecdysone-responsive, estrogen-responsive, and glutacorticoid-responsive promoters), tetracycline “Tet-On” and “Tet-Off” systems, and metal-responsive promoters.

The polynucleotide sequence according to one embodiment disclosed in the present application may be present in a vector in which the polynucleotide sequence is operably linked to regulatory sequences capable of providing for the expression of the polynucleotide sequence by a suitable host cell.

According to one embodiment disclosed in the present application, the polynucleotide sequence may be selected from the following groups:

1) a polynucleotide sequence, in which any one polynucleotide sequence selected from the group consisting of SEQ ID NOs: 241-480 and 823, preferably SEQ ID NOs: 242, 252, 274, 279, 322, 331, 338, 345, 347, 361, 365, 370, 371, 383, 387, 417, 462, 468, 469 and 823, more preferably SEQ ID NO: 252 and 361, is operably linked with a polynucleotide sequence of SEQ ID NO: 817; and

2) a polynucleotide sequence, in which any one polynucleotide sequence selected from the group consisting of SEQ ID NOs: 805 to 811 is further operably linked to the polynucleotide sequence of 1), or further operably linked to between: any one polynucleotide sequence selected from the group consisting of SEQ ID NOs: 241-480 and 823, preferably SEQ ID NOs: 242, 252, 274, 279, 322, 331, 338, 345, 347, 361, 365, 370, 371, 383, 387, 417, 462, 468, 469 and 823, more preferably SEQ ID NO: 252 and 361; and a polynucleotide sequence of SEQ ID NO: 817.

Within an expression vector, the term “operably linked” is intended to mean that the polynucleotide sequence of interest is linked to the regulatory sequence(s) in a manner which allows for expression of the polynucleotide sequence. The term “regulatory sequence” is intended to include promoters, enhancers, and other expression control elements. Such operable linkage with the expression vector can be achieved by conventional gene recombination techniques known in the art, while site-directed DNA cleavage and linkage are carried out by using conventional enzymes known in the art.

The expression vectors may contain a signal sequence or a leader sequence for membrane targeting or secretion, as well as regulatory sequences such as a promoter, an operator, an initiation codon, a termination codon, a polyadenylation signal, an enhancer and the like. The promoter may be a constitutive or an inducible promoter. Further, the expression vector may include one or more selectable marker genes for selecting the host cell containing the expression vector, and may further include a polynucleotide sequence that enables the vector to replicate in the host cell in question.

The expression vector constructed according to one embodiment disclosed in the present application may be the vector where the polynucleotide encoding the CP-ΔSOCS3 recombinant protein (where an aMTD is fused to the N-terminus or C-terminus of a ΔSOCS3 protein) is inserted within the multiple cloning sites (MCS), preferably within the Nde1/BamH1 site or BamH1/Sal1 site of a pET-28a(+)(Novagen, USA) or pET-26b(+) vector(Novagen, USA).

In still another embodiment disclosed in the present application, the polynucleotide encoding the SD being additionally fused to the N-terminus or C-terminus of a ΔSOCS3 protein or an aMTD may be inserted into a cleavage site of restriction enzyme (Nde1, BamH1 and Sal1, etc.) within the multiple cloning sites (MCS) of a pET-28a(+)(Novagen, USA) or pET-26b(+) vector(Novagen, USA).

In still another embodiment disclosed in the present application, the polynucleotide encoding the CP-ΔSOCS3 recombinant protein may be cloned into a pET-28a(+) vector bearing a His-tag sequence so as to fuse six histidine residues to the N-terminus of the CP-ΔSOCS3 recombinant protein to allow easy purification.

According to one embodiment disclosed in the present application, the polynucleotide sequence may be a polynucleotide sequence represented by SEQ ID NO: 819.

According to another embodiment disclosed in the present application, the polynucleotide sequence may be further fused with SD, and may be represented by a polynucleotide sequence represented by SEQ ID NOs: 821.

The recombinant protein may be introduced into an appropriate host cell, e.g., a bacterial cell, a yeast cell, an insect cell, or a tissue culture cell. The recombinant protein may also be introduced into embryonic stem cells in order to generate a transgenic organism. Large numbers of suitable vectors and promoters are known to those skilled in the art and are commercially available for generating the recombinant protein.

Known methods may be used to construct vectors including the polynucleotide sequence according to one embodiment disclosed in the present application and appropriate transcriptional/translational control signals. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo recombination/genetic recombination. For example, these techniques are described in the literatures [Sambrook & Russell, Molecular Cloning: A Laboratory Manual, 3d Edition, Cold Spring Harbor Laboratory, N.Y. (2001); and Ausubel et al., Current Protocols in Molecular Biology Greene Publishing Associates and Wiley Interscience, N.Y. (1989)].

Still another aspect disclosed in the present application provides a transformant transformed with the recombinant expression vector.

The transformation includes transfection, and refers to a process whereby a foreign (extracellular) DNA, with or without an accompanying material, enters into a host cell. The “transfected cell” refers to a cell into which the foreign DNA is introduced into the cell, and thus the cell harbors the foreign DNA. The DNA may be introduced into the cell so that a nucleic acid thereof may be integrated into the chromosome or replicable as an extrachromosomal element. The cell introduced with the foreign DNA, etc. is called a transformant.

As used herein, ‘introducing’ of a protein, a peptide, an organic compound into a cell may be used interchangeably with the expression of ‘carrying,’ ‘penetrating,’ ‘transporting,’ ‘delivering,’ ‘permeating’ or ‘passing.’

It is understood that the host cell refers to a eukaryotic or prokaryotic cell into which one or more DNAs or vectors are introduced, and refers not only to the particular subject cell but also to the progeny or potential progeny thereof. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.

The host cells may be preferably bacterial cells, and as the bacterial cells, there are, in principle, no limitations. They may be eubacteria (gram-positive or gram-negative) or archaebacteria, as long as they allow genetic manipulation for insertion of a gene of interest, preferably for site-specific integration, and they may be cultured on a manufacturing scale. Preferably, the host cells may have the property to allow cultivation to high cell densities.

Examples of bacterial host cells that may be used in the preparation of the recombinant protein are E. coli (Lee, 1996; Hannig and Makrides, 1998), Bacillus subtilis, Pseudomonas fluorescens (Squires et al., 2004; Retallack et al., 2006) as well as various Corynebacterium (US 2006/0003404 A1) and Lactococcus lactis (Mierau et al., 2005) strains. Preferably, the host cells are Escherichia coli cells.

More preferably, the host cell may include an RNA polymerase capable of binding to a promoter regulating the gene of interest. The RNA polymerase may be endogenous or exogenous to the host cell.

Preferably, host cells with a foreign strong RNA polymerase may be used. For example, Escherichia coli strains engineered to carry a foreign RNA polymerase (e.g. like in the case of using a T7 promoter a T7-like RNA polymerase in the so-called “T7 strains”) integrated in their genome may be used. Examples of T7 strains, e.g. BL21(DE3), HMS174(DE3), and their derivatives or relatives (see Novagen, pET System manual, 11^(th) edition), may be widely used and commercially available. Preferably, BL21-CodonPlus (DE3)-RIL or BL21-CodonPlus (DE3)-RIPL (Agilent Technologies) may be used. These strains are DE3 lysogens containing the T7 RNA polymerase gene under control of the lacUV5 promoter. Induction with IPTG allows production of T7 RNA polymerase which then directs the expression of the gene of interest under the control of the T7 promoter.

The host cell strains, E. coli BL21(DE3) or HMS174(DE3), which have received their genome-based T7 RNA polymerase via the phage DE3, are lysogenic. It is preferred that the T7 RNA polymerase contained in the host cell has been integrated by a method which avoids, or preferably excludes, the insertion of residual phage sequences in the host cell genome since lysogenic strains have the disadvantage to potentially exhibit lytic properties, leading to undesirable phage release and cell lysis.

Still another aspect disclosed in the present application provides a preparing method of the CP-ΔSOCS3 recombinant protein including preparing the recombinant expression vector; preparing the transformant using the recombinant expression vector; culturing the transformant; and recovering the recombinant protein expressed by culturing.

Culturing may be preferably in a mode that employs the addition of a feed medium, this mode being selected from the fed-batch mode, semi-continuous mode, or continuous mode, and the bacterial expression host cells may include a DNA construct, integrated in their genome, carrying the DNA sequence encoding the protein of interest under the control of a promoter that enables expression of said protein.

There are no limitations in the type of the culture medium. The culture medium may be semi-defined, i.e. containing complex media compounds (e.g. yeast extract, soy peptone, casamino acids), or it may be chemically defined, without any complex compounds. Preferably, a defined medium may be used. The defined media (also called minimal or synthetic media) are exclusively composed of chemically defined substances, i.e. carbon sources such as glucose or glycerol, salts, vitamins, and, in view of a possible strain auxotrophy, specific amino acids or other substances such as thiamine. Most preferably, glucose may be used as a carbon source. Usually, the carbon source of the feed medium serves as the growth-limiting component which controls the specific growth rate.

Host cells may be disrupted by any convenient method, including freeze-thaw cycling, sonication, mechanical disruption, or the use of cell lysing agents. The literature [Scopes, Protein Purification: Principles and Practice, New York: Springer-Verlag (1994)] describes a number of general methods for purifying recombinant (and non-recombinant) proteins. The methods may include, e.g., ion-exchange chromatography, size-exclusion chromatography, affinity chromatography, selective precipitation, dialysis, and hydrophobic interaction chromatography. These methods may be adapted to devise a purification strategy for the cell permeable recombinant protein. If the cell permeable recombinant protein includes a purification handle, such as an epitope tag or a metal chelating sequence, affinity chromatography may be used to easily purify the protein.

The amount of the protein produced may be evaluated by detecting the advanced macromolecule transduction domain directly (e.g., using Western analysis) or indirectly (e.g., by assaying materials derived from the cells for specific DNA binding activity, such as by electrophoretic mobility shift assay). Proteins may be detected prior to purification, during any stage of purification, or after purification. In some implementations, purification or complete purification may not be necessary.

The CP-ΔSOCS3 recombinant proteins according to one embodiment disclosed in the present application are cell permeable proteins, and may be used as protein-based vaccines, particularly in the case where killed or attenuated whole organism vaccines are impractical.

The CP-ΔSOCS3 recombinant proteins according to one embodiment disclosed in the present application may be preferably used for the prevention or treatment of obesity, diabetes or comorbidities thereof. The cell permeable recombinant proteins may be delivered to the interior of the cell, eliminating the need to transfect or transform the cell with a recombinant vector. The cell permeable recombinant proteins may be used in vitro to investigate protein function or may be used to maintain cells in a desired state.

Still another aspect disclosed in the present application provides a composition including the CP-ΔSOCS3 Recombinant Protein as an active ingredient.

According to one embodiment disclosed in the present application, the composition may be for use in control of appetite, feeding, food intake, energy expenditure and calorie intake, the composition comprising an effective amount of a recombinant protein according to the present invention.

Still another aspect disclosed in the present application provides a pharmaceutical composition for treating or preventing obesity, eating disorders, diabetes or a symptom of diabetes, or comorbidities associated with obesity or excess weight including the CP-ΔSOCS3 Recombinant Protein as an active ingredient; and a pharmaceutically acceptable carrier.

According to one embodiment disclosed in the present application, the CP-ΔSOCS3 Recombinant Protein may be used in combination with another therapeutic agent such as appetite-suppressing agent or satiety-inducing agent including leptin, Belviq, Qsymia, Xenical, Saxenda, Contrave, etc.

Obesity is a medical condition in which excess body fat has accumulated to the extent that it may have a negative effect on health. It is a serious metabolic disease of the modern and is characterized by low-level chronic inflammation. Obesity affects not only simply physical activity but also psychological aspect.

The term “Obesity” also includes conditions or disorders associated with increased caloric intake. The conditions or disorders include, but are not limited to, leptin-resistance, insulin resistance, glucose intolerance, obesity, diabetes including type 2 (non-insulin dependent) diabetes, eating disorders, and insulin-resistance syndromes.

Preferably, the composition may be for injectable (e.g. intraperitoneal, intravenous, and intra-arterial, etc.) and may include the active ingredient in an amount of 0.05 mg/kg to 2.5 mg/kg, preferably 0.1 mg/kg to 2 mg/kg, more preferably 0.1 mg/kg to 1.25 mg/kg for human.

For examples, dosages per day normally fall within the range of about 0.05 to about 2.5 mg/kg of body weight. In the treatment of adult humans, the range of about 0.1 to about 1.25 mg/kg/day, in single or divided dose, is especially preferred. However, it will be understood that the concentration of the CP-ΔSOCS3 recombinant protein actually administered will be determined by a physician, in the light of the relevant circumstances, including the condition to be treated, the chosen route of administration, the age, weight, and response of the individual patient, and the severity of the patient's symptoms, and therefore the above dosage ranges are not intended to limit the scope of the invention in any way. In some instances dosage levels below the lower limit of the aforesaid range may be more than adequate, while in other cases still larger doses may be employed without causing any harmful side effect, provided that such larger doses are first divided into several smaller doses for administration throughout the day.

Still another aspect disclosed in the present application provides use of the CP-ΔSOCS3 recombinant protein as a medicament for treating or preventing of obesity or diabetes.

Still another aspect disclosed in the present application provides use of the CP-ΔSOCS3 recombinant protein as a medicament for the reduction of appetite, food intake, calorie intake, body weight or body weight gain in a subject, or the increase of energy expenditure in a subject.

Still another aspect disclosed in the present application provides a medicament including the CP-ΔSOCS3 recombinant protein.

Still another aspect disclosed in the present application provides use of the CP-ΔSOCS3 recombinant protein for the preparation of a medicament for treating or preventing obesity or diabetes.

Still another aspect disclosed in the present application provides a method of treating or preventing obesity or diabetes in a subject including identifying a subject in need of treatment or prevention of obesity or diabetes; and administering to the subject a therapeutically effective amount of the CP-ΔSOCS3 recombinant protein.

Still another aspect disclosed in the present application provides a method of reducing appetite, food intake, calorie intake, body weight or body weight gain in a subject; or increasing energy expenditure in a subject comprising administering to the subject the CP-ΔSOCS3 recombinant protein.

In one embodiment disclosed in the present application, the subject may be preferably a mammal.

Preferably, the subject may be overweight, for example, which may be due to leptin resistance.

Alternatively, or in addition thereto, the subject may be diabetic, for example having insulin resistance or glucose intolerance, or both. The subject may have diabetes mellitus, for example, such as Type 2 diabetes.

In addition, or alternatively, the subject may have, or may be at risk of having, a disorder in which obesity or being overweight is a risk factor. Such disorders include, but are not limited to, cardiovascular disease, for example hypertension, atherosclerosis, congestive heart failure, and dyslipidemia; stroke; gallbladder disease; reduced fertility; osteoarthritis; sleep apnea; reproductive disorders for example, polycystic ovarian syndrome; cancers, for example breast, prostate, colon, endometrial, kidney, and esophagus cancer; varicose veins; acanthosis nigricans; eczema; exercise intolerance; hypercholesterolemia; cholithiasis; orthopedic injury; leptin resistance; insulin resistance, for example, type 2 diabetes and syndrome X; metabolic syndrome; and thromboembolic disease.

The pharmaceutical composition according to one embodiment disclosed in the present application may be prepared by using pharmaceutically suitable and physiologically acceptable additives, in addition to the active ingredient, and the additives may include excipients, disintegrants, sweeteners, binders, coating agents, blowing agents, lubricants, glidants, flavoring agents, etc.

For administration, the pharmaceutical composition may be preferably formulated by further including one or more pharmaceutically acceptable carriers in addition to the above-described active ingredient.

Dosage forms of the pharmaceutical composition may include granules, powders, tablets, coated tablets, capsules, suppositories, liquid formulations, syrups, juice, suspensions, emulsions, drops, injectable liquid formulations, etc. For formulation of the composition into a tablet or capsule, for example, the active ingredient may be combined with any oral, non-toxic pharmaceutically acceptable inert carrier, such as ethanol, glycerol, water, etc. If desired or necessary, suitable binders, lubricants, disintegrants, and colorants may be additionally included as a mixture.

Examples of the suitable binder may include, but are not limited to, starch, gelatin, natural sugars such as glucose or beta-lactose, corn sweeteners, natural and synthetic gums such as acacia, tragacanth, or sodium oleate, sodium stearate, magnesium stearate, sodium benzoate, sodium acetate, sodium chloride, etc. Examples of the disintegrant may include, but are not limited to, starch, methyl cellulose, agar, bentonite, xanthan gum, etc. For formulation of the composition into a liquid preparation, a pharmaceutically acceptable carrier which is sterile and biocompatible may be used, such as saline, sterile water, a Ringer's solution, buffered saline, an albumin infusion solution, a dextrose solution, a maltodextrin solution, glycerol, and ethanol, and these materials may be used alone or in any combination thereof. If necessary, other common additives, such as antioxidants, buffers, bacteriostatic agents, etc., may be added. Further, diluents, dispersants, surfactants, binders, and lubricants may be additionally added to prepare injectable formulations such as aqueous solutions, suspensions, and emulsions, or pills, capsules, granules, or tablets. Furthermore, the composition may be preferably formulated, depending upon diseases and ingredients, using any appropriate method known in the art, as disclosed in Remington's Pharmaceutical Science, Mack Publishing Company, Easton Pa.

Preferably, the treatment or treating mean improving or stabilizing the subject's condition or disease; or preventing or relieving the development or worsening of symptoms associated with the subject's condition or disease.

The prevention, prophylaxis and preventive treatment are used herein as synonyms. They include the administration of a drug to individuals, in whom at least one symptoms of obesity, diabetes or comorbidities thereof as described above are not only rudimentarily but partially present, in order to prevent or delay the occurrence or significant degree of obesity, diabetes or comorbidities thereof.

The subject and patient are used herein interchangeably. They refer to a human or another mammal (e.g., mouse, rat, rabbit, dog, cat, cattle, swine, sheep, horse or primate) that can be afflicted with or is susceptible to a disease or disorder but may or may not have the disease or disorder. In certain embodiments, the subject is a human being.

Preferably, the amount effective or effective amount is the amount of an active ingredient or a pharmaceutical composition disclosed herein that when administered to a subject for treating a disease, is sufficient to effect such treatment of the disease. Any improvement in the patient is considered sufficient to achieve treatment. An effective amount of an active ingredient or a pharmaceutical composition disclosed herein, used for the treatment of obesity or diabetes can vary depending upon the manner of administration, the age, body weight, and general health of the patient. Ultimately, the prescribers or researchers will decide the appropriate amount and dosage regimen.

In the treatment or prevention method according to one embodiment disclosed in the present application, the composition including the CP-ΔSOCS3 recombinant protein as an active ingredient may be administered in a common manner via oral, buccal, rectal, intravenous, intra-arterial, intraperitoneal, intramuscular, intrasternal, percutaneous, topical, intraocular or subcutaneous route, more preferably via intraperitoneal, intravenous, or intra-arterial injection route.

Advantageous Effects

According to one aspect disclosed in the present application, development and establishment of cell-permeable ΔSOCS3 recombinant protein, as therapeutics of leptin resistance and obesity are provided. Because CP-ΔSOCS3 was designed based on endogenous proteins, it would be a safety anti-obesity drug without side-effect.

However, the effects disclosed in the present application are not limited to the above-mentioned effects, and another effects not mentioned will be clearly understood by those skilled in the art from the following description.

DESCRIPTION OF DRAWINGS

FIG. 1 shows Structure of aMTD- or rPeptide-Fused Recombinant Proteins. A schematic diagram of the His-tagged CRA recombinant proteins is illustrated and constructed according to the present invention. The his-tag for affinity purification (white), aMTD or rPeptide (gray) and cargo A (CRA, black) are shown.

FIG. 2a shows Construction of Expression Vectors for aMTDs- or rPeptide-Fused Recombinant Proteins. FIGS. 2b and 2c show the agarose gel electrophoresis analysis showing plasmid DNA fragments at 645 bp insert encoding aMTDs or rPeptide-fused CRA cloned into the pET28a(+) vector according to the present invention.

FIGS. 3a to 3d show Inducible Expression of aMTD- or rPeptide-Fused Recombinant Proteins. Expressed recombinant aMTD- or random peptide-fused CRA recombinant proteins were transformed in E. coli BL21 (DE3) strain. Expression of recombinant proteins in E. coli before (−) and after (+) induction with IPTG was monitored by SDS-PAGE, and stained with Coomassie blue.

FIGS. 4a and 4b show Purification of aMTD- or rPeptide-Fused Recombinant Proteins. Expressed recombinant proteins were purified by Ni²+ affinity chromatography under the natural condition. Purification of recombinant proteins displayed through SDS-PAGE analysis.

FIGS. 5a to 5u show Determination of aMTD-Mediated Cell-Permeability. Cell-permeability of a negative control (A: rP38) and reference hydrophobic CPPs (MTM12 and MTD85) are shown. The cell-permeability of each aMTD and/or rPeptide is visually compared to that of the cargo protein lacking peptide sequence (HCA). Gray shaded area represents untreated RAW 264.7 cells (vehicle); thin light gray line represents the cells treated with equal molar concentration of FITC (FITC only); dark thick line indicates the cells treated with FITC-his-tagged CRA protein (HCA); and the cells treated with the FITC-proteins (HMCA) fused to negative control (rP38), reference CPP (MTM12 or MTD85) or new hydrophobic CPP (aMTD) are shown with light thick line and indicated by arrows.

FIGS. 6a to 6c show Determination of rPeptide-Mediated Cell-Permeability. The cell-permeability of each aMTD and/or rPeptide was visually compared to that of the cargo protein lacking peptide sequence (HCA). Gray shaded area represents untreated RAW 264.7 cells (vehicle); thin light gray line represents the cells treated with equal molar concentration of FITC (FITC only); dark thick line indicates the cells treated with FITC-his-tagged CRA protein (HCA); and the cells treated with the FITC-proteins fused to rPeptides are shown with light thick line and indicated by arrows.

FIGS. 7a to 7k shows Visualized Cell-Permeability of aMTD-Fused Recombinant Proteins. NIH3T3 cells were treated with FITC-labeled protein (10 μl M) fused to aMTD for 1 hour at 37. Cell-permeability of the proteins was visualized by laser scanning confocal microscopy (LSM700 version).

FIG. 8 show Visualized Cell-Permeability of rPeptide-Fused Recombinant Proteins. Cell-permeability of rPeptide-fused recombinant proteins was visualized by laser scanning confocal microscopy (LSM700 version).

FIGS. 9a to 9c show Relative Cell-Permeability of aMTD-Fused Recombinant Proteins Compared to Negative Control (rP38). The FIG shows graphs comparing the cell-permeability of the recombinant proteins fused to aMTDs and a negative control (A: rP38).

FIGS. 10a to 10c show Relative Cell-Permeability of aMTD-Fused Recombinant Proteins Compared to Reference CPP (MTM12). The FIG shows graphs comparing the cell-permeability of the recombinant proteins fused to aMTDs and a reference CPP (MTM12).

FIGS. 11a to 11c show Relative Cell-Permeability of aMTD-Fused Recombinant Proteins Compared to Reference CPP (MTD85). The FIG shows graphs comparing the cell-permeability of the recombinant proteins fused to aMTDs and a reference CPP (MTD85).

FIG. 12 shows Relative Cell-Permeability of rPeptide-Mediated Recombinant Proteins Compared to Average that of aMTDs. The FIG shows graphs comparing the cell-permeability of the recombinant proteins fused to rPeptides and that (average value: aMTD AVE) of aMTDs.

FIGS. 13a to 13d show Association of Cell-Permeability with Amino Acid Composition in aMTD Sequences. These graphs display delivery potential (Geometric Mean) of aMTDs influenced with amino acid composition (A, I, V and L).

FIGS. 14a to 14d show Association of Cell-Permeability with Critical Factors in aMTDs. These graphs show the association of cell-permeability with critical factors [bending potential: proline position (PP), rigidity/flexibility: instability index (II), structural feature: aliphatic index (AI) and hydropathy: grand average of hydropathy (GRAVY)].

FIGS. 15a to 15d show Relative Relevance of aMTD-Mediated Cell-Permeability with Critical Factors. Cell-permeability of 10 high and 10 low ranked aMTDs in their delivery potential were examined for their association with the critical factors [bending potential: proline position (PP), rigidity/flexibility: instability index (II), structural feature: aliphatic index (AI) and hydropathy: grand average of hydropathy (GRAVY)].

FIG. 16 shows Relative Relevance of rPeptide-Mediated Cell-Permeability with Hydropathy Range (GRAVY). This graph and a chart illustrate relative relevance of rPeptide-mediated cell-permeability with its hydropathy range (GRAVY).

FIG. 17 shows a schematic Diagram of ΔSOCS3.

FIG. 18 shows a structure of CP-ΔSOCS3 designed according to example 6-3.

FIG. 19 shows the agarose gel electrophoresis analysis showing plasmid DNA fragments insert encoding His-ΔSOCS3 (1), His-aMTD₂₄-ΔSOCS3 (2), His-aMTD₂₄-ΔSOCS3-SDA (3), and His-aMTD₂₄-ΔSOCS3-SDB (4) cloned into the pET28a (+) vector according to example 6-4.

FIG. 20 shows expression, purification and the solubility/yield of His-ΔSOCS3 (A53-1), His-aMTD₂₄-ΔSOCS3 (ΔS3-2), His-aMTD₂₄-ΔSOCS3-SDA (ΔS3-3), and His-aMTD₂₄-ΔSOCS3-SDB (ΔS3-4) in E. coli according to example 6-4.

FIG. 21 shows solubility/yield and permeability of CP-ΔSOCS3 Recombinant Proteins prepared by various aMTD according to example 6-4.

FIG. 22 shows induction of his-tag lacking CP-ΔSOCS3 (aMTD₅₂₂-ΔSOCS3-SDB) recombinant protein according to example 6-4.

FIG. 23 shows cell-permeability of CP-ΔSOCS3 recombinant proteins (His-aMTD₅₂₂-ΔSOCS3-SDB and His-ΔSOCS3-SDB) in LN229 cell compared to non-CP-ΔSOCS3 to according to example 7-1.

FIG. 24 shows aMTD-Mediated intracellular localization of CP-ΔSOCS3 according to example 7-2.

FIG. 25 shows that the CP-ΔSOCS3 recombinant protein directly binds to ObR according to example 8-1.

FIGS. 26 and 27 show phosphorylation of JAK2 and STAT3 by leptin in NIH3T3 cell (FIG. 26) and LN229 cell (FIG. 27) according to example 8-2-1.

FIG. 28 shows that CP-ΔSOCS3 recombinant protein enhances leptin signaling in vitro in a dose-dependent manner according to example 8-2-2.

FIG. 29 shows that CP-ΔSOCS3 recombinant protein enhances leptin signaling in hypothalamus of normal mice according to example 8-2-3.

FIG. 30 shows that CP-ΔSOCS3 recombinant protein enhances leptin signaling in hypothalamus of diet-induced obese mice according to example 8-2-3.

FIG. 31 shows reduction of body weight of obese mice by treating CP-ΔSOCS3 recombinant protein with leptin according to example 8-3-1.

FIG. 32 shows increase of serum leptin level in mice by high-fat diet according to example 8-3-1.

FIG. 33 shows reduction of serum leptin level in obese mice by combination treatment of CP-ΔSOCS3 recombinant protein and leptin according to example 8-3-1.

FIG. 34 shows reduction of body weight of obese mice by CP-ΔSOCS3 recombinant protein monotherapy according to example 8-3-2.

FIG. 35 shows reduction of body weight of obese mice by injecting (IP or IV) CP-ΔSOCS3 recombinant protein in regulated-fat diet condition (top) and in high-fat diet condition (bottom) according to example 8-3-2.

FIG. 36 shows reduction of food intake of obese mice by injecting (IP or IV) CP-ΔSOCS3 recombinant protein in regulated-fat diet condition (top) and in high-fat diet condition (bottom) according to example 8-3-2.

FIG. 37 shows that CP-ΔSOCS3 recombinant protein improves glycemic control of obese mice according to example 8-3-3.

FIG. 38 shows reduction of lipid accumulation in liver of obese mice by IV injection of CP-ΔSOCS3 recombinant protein in regulated-fat diet condition (top) and in high-fat diet condition (bottom) according to example 8-3-4.

MODE FOR INVENTION

1. Analysis of Reference Hydrophobic CPPs to Identify ‘Critical Factors’ for Development of Advanced MTDs

Previously reported MTDs were selected from a screen of more than 1,500 signal peptide sequences. Although the MTDs that have been developed did not have a common sequence or sequence motif, they were all derived from the hydrophobic (H) regions of signal sequences (HRSSs) that also lack common sequences or motifs except their hydrophobicity and the tendency to adopt alpha-helical conformations. The wide variation in H-region sequences may reflect prior evolution for proteins with membrane translocating activity and subsequent adaptation to the SRP/Sec61 machinery, which utilizes a methionine-rich signal peptide binding pocket in SRP to accommodate a wide-variety of signal peptide sequences.

Previously described hydrophobic CPPs (e.g. MTS/MTM and MTD) were derived from the hydrophobic regions present in the signal peptides of secreted and cell surface proteins. The prior art consists first, of ad hoc use of H-region sequences (MTS/MTM), and second, of H-region sequences (with and without modification) with highest CPP activity selected from a screen of 1,500 signal sequences (MTM). Second prior art, the modified H-region derived hydrophobic CPP sequences had advanced in diversity with multiple number of available sequences apart from MTS/MTM derived from fibroblast growth factor (FGF) 4. However, the number of MTDs that could be modified from naturally occurring secreted proteins are somewhat limited. Because there is no set of rules in determining their cell-permeability, no prediction for the cell-permeability of modified MTD sequences can be made before testing them.

The hydrophobic CPPs, like the signal peptides from which they originated, did not conform to a consensus sequence, and they had adverse effects on protein solubility when incorporated into protein cargo. We therefore set out to identify optimal sequence and structural determinants, namely critical factors (CFs), to design new hydrophobic CPPs with enhanced ability to deliver macromolecule cargoes including proteins into the cells and tissues while maintaining protein solubility. These newly developed CPPs, advanced macromolecule transduction domains (aMTDs) allowed almost infinite number of possible designs that could be designed and developed based on the critical factors. Also, their cell-permeability could be predicted by their character analysis before conducting any in vitro and/or in vivo experiments. These critical factors below have been developed by analyzing all published reference hydrophobic CPPs.

1-1. Analysis of Hydrophobic CPPs

Seventeen different hydrophobic CPPs (Table 1) published from 1995 to 2014 (Table 2) were selected. After physiological and chemical properties of selected hydrophobic CPPs were analyzed, 11 different characteristics that may be associated with cell-permeability have been chosen for further analysis. These 11 characteristics are as follows: sequence, amino acid length, molecular weight, pI value, bending potential, rigidity/flexibility, structural feature, hydropathy, residue structure, amino acid composition and secondary structure of the sequences (Table 3).

Table 1 shows the summary of published hydrophobic Cell-Penetrating Peptides which were chosen.

TABLE 1 # Peptide Origin Protein Ref. 1 MTM Homo sapiens NP_001998 Kaposi fibroblast growth factor (K-FGF) 1 2 MTS Homo sapiens NP_001998 Kaposi fibroblast growth factor (K-FGF) 2 3 MTD10 Streptomyces coelicolor NP_625021 Glycosyl hydrolase 8 4 MTD13 Streptomyces coelicolor NP_639877 Putative secreted protein 5 5 MTD47 Streptomyces coelicolor NP_627512 Secreted protein 7 6 MTD56 Homo sapiens P23274 Peptidyl-prolyl cis-trans isomerase B precursor 6 7 MTD73 Drosophila melanogaster AAA17887 Spatzle (spz) protein 6 8 MTD77 Homo sapiens NP_003231 Kaposi fibroblast growth factor (K-FGF) 3 9 MTD84 Phytophthora cactorum AAK63068 Phytotoxic protein PcF precusor 7 10 MTD85 Streptomyces coelicolor NP_629842 Peptide transport system peptide binding 5 protein 11 MTD86 Streptomyces coelicolor NP_629842 Peptide transport system secreted peptide 7 binding protein 12 MTD103 Homo sapiens TMBV19 domain Family member B 4 13 MTD132 Streptomyces coelicolor NP_628377 P60-family secreted protein 7 14 MTD151 Streptomyces coelicolor NP_630126 Secreted chitinase 8 15 MTD173 Streptomyces coelicolor NP_624384 Secreted protein 7 16 MTD174 Streptomyces coelicolor NP_733505 Large, multifunctional secreted protein 8 17 MTD181 Neisseria meningitidis Z2491 CAB84257.1 Putative secreted protein 7

Table 2 summarizes reference information

TABLE 2 References # Title Journal Year Vol Issue Page 1 Inhibition of Nuclear Translocation of Transcription Factor JOURNAL OF 1995 270 24 14255 NF-kB by a Synthetic peptide Containing a Cell Membrane- BIOLOGICAL permeable Motif and Nuclear Localization Sequence CHEMISTRY 2 Epigenetic Regulation of Gene Structure and Function with NATURE 2001 19 10 929 a Cell-Permeable Cre Recombinase BIOTECHNOLOGY 3 Cell-Permeable NM23 Blocks the Maintenance and CANCER 2011 71 23 7216 Progression of Established Pulmonary Metastasis RESEARCH 4 Antitumor Activity of Cell-Permeable p18INK4c With MOLECULAR 2012 20 8 1540 Enhanced Membrane and Tissue Penetration THERAPY 5 Antitumor Activity of Cell-Permeable RUNX3 Protein in CLINICAL 2012 19 3 680 Gastric Cancer Cells CANCER RESEARCH 6 The Effect of Intracellular Protein Delivery on the Anti- BIOMATERIALS 2013 34 26 6261 Tumor Activity of Recombinant Human Endostatin 7 Partial Somatic to Stem Cell Transformations Induced By SCIENTIFIC 2014 4 10 4361 Cell-Permeable Reprogramming Factors REPORTS 8 Cell-Permeable Parkin Proteins Suppress Parkinson PLOS ONE 2014 9 7 17 Disease-Associated Phenotypes in Cultured Cells and Animals

Table 3 shows characteristics of published hydrophobic Cell-Penetrating Peptides (A) which were analyzed.

TABLE 3 Rigidity/ Structural SEQ Mole- Flexibility Feature ID cular Bending (Instability (Aliphatic BIS Peptide Sequence Length Weight pI Potential Index: II) index: AI) 852 MTM AAVALLPAVLLALLAP 16 1,515.3 5.6 Bending 46.5 220.0 853 MT5 AAVLLPVLLAAP 12 1,147.4 5.6 Bending 57.3 211.7 854 MTD10 LGGAVVAAPVAAAVAP 16 1,333.5 5.5 Bending 47.9 140.6 855 MTD13 LAAAALAVLPL 11 1,022.3 3.5 Bending 26.6 213.6 856 MTD47 AAAVPVLVAA 10   891.0 5.6 Bending 47.5 176.0 857 MTD56 VLLAAALIA  9   954.1 6.5 No-  6.9 250.0 Bending 858 MTD73 PVLLLLA  7   737.9 6.0 No 36.1 276.6 Bending 859 MTD77 AVALLLAV  9   882.0 5.6 No- 30.3 271.1 Bending 860 MTD84 AVALVAVVAVA 11   962.2 5.6 No-  9.1 212.7 Bending 861 MTD85 LLAAAAALLIA 11 1,010.2 5.5 No-  9.1 231.8 Bending 861 MTD88 LLAAAAALLLA 11 1,010.2 6.5 No-  8.1 231.8 Bending 863 MTD103 LALPVLLLA  8   922.2 5.5 Bending 51.7 271.1 864 MTD132 AVVVPAIVLAAP 12 1,119.4 5.6 Bending 50.3 195.0 865 MTD151 AAAPVAAVP  9 1,031.4 5.5 Bending 73.1 120.0 866 MTD173 AVIPILAVP  9   892.1 5.6 Bending 48.5 216.7 867 MTD174 LLLLPAVALP 11 1,011.8 5.5 Bending 79.1 257.3 868 MTD181 AVLLLPAAA  9   838.8 5.6 Bending 51.7 206.7 AVE 10.8 ± 1,011 ±   5.6 ± Proline  43.1 ±   217.9 ± 2.4   189.6 0.1 Presence 21.8  43.6 SEQ Hydro- ID pathy Residue A/a Composition Secondary NOS (GRAVY) Structure A V L I P G Structure Cargo Ret. 852 2.4 Aliphatic 6 2 6 0 2 0 Helix p53 1 Ring 853 2.3 Aliphatic 2 4 2 9 2 0 No-Helix CRE 2 Ring 854 1.9 Aliphatic 7 4 1 0 2 2 Helix Parkin 8 Ring 855 2.4 Aliphatic 5 1 4 9 1 0 No-Helix RUNX3 3 Ring 856 2.4 Aliphatic 5 3 1 8 1 0 No-Helix CMYC 7 Ring 857 3.9 Aliphatic 4 1 3 1 6 0 Helix ES 6 Ring 858 2.8 Aliphatic 1 1 4 0 1 0 Helix ES 6 Ring 859 3.3 Aliphatic 3 2 3 1 3 0 Helix NM23 3 Ring 860 2.7 Aliphatic 8 3 5 0 3 0 No-Helix RUNX3 5 Ring 861 2.7 Aliphatic 5 6 5 9 3 0 No-Helix SOX2 7 Ring 862 2.8 Aliphatic 2 1 5 0 1 0 Helix p18 4 Ring 863 2.4 Aliphatic 4 4 1 1 2 0 No-Helix LIN28 7 Ring 864 1.6 Aliphatic 5 2 0 9 2 0 No-Helix Parkin 8 Ring 865 2.4 Aliphatic 2 2 1 2 2 0 Helix KLF4 7 Ring 866 2.6 Aliphatic 2 2 1 2 2 0 Helix KLF4 7 Ring 867 2.6 Aliphatic 2 1 5 1 2 0 Helix Parkin 8 Ring 868 2.4 Aliphatic 4 1 3 0 1 0 No-Helix SOX2 7 Ring AVE   2.5 ± 0.4

Two peptide/protein analysis programs were used (ExPasy: SoSui: http://harrier.nagahama-i-bio.ac.jp/sosui/sosui_submit.html) to determine various indexes and structural features of the peptide sequences and to design new sequence. Followings are important factors analyzed.

1-2. Characteristics of Analyzed Peptides: Length, Molecular Weight and pl Value

Average length, molecular weight and pl value of the peptides analyzed were 10.8±2.4, 1,011±189.6 and 5.6±0.1, respectively (Table 4)

Table 4 summarizes Critical Factors (CFs) of published hydrophobic Cell-Penetrating Peptides (A) which were analyzed.

TABLE 4 Length: 10.8 ± 2.4 Molecular Weight: 1,011 ± 189.6 pI: 5.6 ± 0.1 Bending Potential (BP): Proline presences in the middle and/or the end of peptides, or No Proline. Instability Index (II): 40.1 ± 21.9 Residue Structure & Aliphatic Index (AI): 217.9 ± 43.6 Hydropathy (GRAVY): 2.5 ± 0.4 Aliphatic Ring: Non-polar hydrophobic & aliphatic amino acid (A, V, L, I). Secondary Structure: α-Helix is favored but not required.

1-3. Characteristics of Analyzed Peptides: Bending Potential—Proline Position (PP)

Bending potential (bending or no-bending) was determined based on the fact whether proline (P) exists and/or where the amino acid(s) providing bending potential to the peptide in recombinant protein is/are located. Proline differs from the other common amino acids in that its side chain is bonded to the backbone nitrogen atom as well as the alpha-carbon atom. The resulting cyclic structure markedly influences protein architecture which is often found in the bends of folded peptide/protein chain.

Eleven out of 17 were determined as ‘Bending’ peptide which means that proline is present in the middle of sequence for peptide bending and/or located at the end of the peptide for protein bending. As indicated above, peptide sequences could penetrate the plasma membrane in a “bent” configuration. Therefore, bending or no-bending potential is considered as one of the critical factors for the improvement of current hydrophobic CPPs.

1-4. Characteristics of Analyzed Peptides: Rigidity/Flexibility—Instability Index (II)

Since one of the crucial structural features of any peptide is based on the fact whether the motif is rigid or flexible, which is an intact physicochemical characteristic of the peptide sequence, instability index (II) of the sequence was determined. The index value representing rigidity/flexibility of the peptide was extremely varied (8.9-79.1), but average value was 40.1±21.9 which suggested that the peptide should be somehow flexible, but not too much rigid or flexible (Table 3).

1-5. Characteristics of Analyzed Peptides: Structural Features—Structural Feature (Aliphatic Index: AI) and Hydropathy (Grand Average of Hydropathy: GRAVY)

Alanine (V), valine (V), leucine (L) and isoleucine (I) contain aliphatic side chain and are hydrophobic—that is, they have an aversion to water and like to cluster. These amino acids having hydrophobicity and aliphatic residue enable them to pack together to form compact structure with few holes. Analyzed peptide sequence showed that all composing amino acids were hydrophobic (A, V, L and I) except glycine (G) in only one out of 17 (MTD10-Table 3) and aliphatic (A, V, L, I, and P). Their hydropathic index (Grand Average of Hydropathy: GRAVY) and aliphatic index (AI) were 2.5±0.4 and 217.9±43.6, respectively. Their amino acid composition is also indicated in the Table 3.

1-6. Characteristics of Analyzed Peptides: Secondary Structure (Helicity)

As explained above, the CPP sequences may be supposed to penetrate the plasma membrane directly after inserting into the membranes in a “bent” configuration with hydrophobic sequences having α-helical conformation. In addition, our analysis strongly indicated that bending potential was crucial for membrane penetration. Therefore, structural analysis of the peptides was conducted to determine whether the sequences were to form helix or not. Nine peptides were helix and eight were not (Table 3). It seems to suggest that helix structure may not be required.

1-7. Determination of Critical Factors (CFs)

In the 11 characteristics analyzed, the following 6 are selected namely “Critical Factors” for the development of new hydrophobic CPPs—advanced MTDs: amino acid length, bending potential (proline presence and location), rigidity/flexibility (instability index: II), structural feature (aliphatic index: AI), hydropathy (GRAVY) and amino acid composition/residue structure (hydrophobic and aliphatic A/a) (Table 3 and Table 4).

2. Analysis of Selected Hydrophobic CPPs to Optimize ‘Critical Factors’

Since the analyzed data of the 17 different hydrophobic CPPs (analysis A, Table 3 and 4) previously developed during the past 2 decades showed high variation and were hard to make common- or consensus-features, analysis B (Table 5 and 6) and C (Table 7 and 8) were also conducted to optimize the critical factors for better design of improved CPPs—aMTDs. Therefore, 17 hydrophobic CPPs have been grouped into two groups and analyzed the groups for their characteristics in relation to the cell permeable property. The critical factors have been optimized by comparing and contrasting the analytical data of the groups and determining the common homologous features that may be critical for the cell permeable property.

2-1. Selective Analysis (B) of Peptides Used to Biologically Active Cargo Protein for In Vivo

In analysis B, eight CPPs were used with each biologically active cargo in vivo. Length was 11±3.2, but 3 out of 8 CPPs possessed little bending potential. Rigidity/Flexibility (instability index: II) was 41±15, but removing one [MTD85: rigid, with minimal II (9.1)] of the peptides increased the overall instability index to 45.6±9.3. This suggested that higher flexibility (40 or higher II) is potentially be better. All other characteristics of the 8 CPPs were similar to the analysis A, including structural feature and hydropathy (Table 5 and 6)

Table 5 shows characteristics of published hydrophobic Cell-Penetrating Peptides (B): selected CPPs that were used to each cargo in vivo.

TABLE 5 Rigidity/ Structural SEQ Flexibility Feature ID Molecular Bending (Instability (Aliphatic NOs Peptides Sequence Length Weight pI Potential Index: II) Index: AI) 852 MTM AAVALLPAVLLALLAP 15 1,515.9 5.0 Bending 45.5 220.0 853 MTS AAVLLPVLLAAP 12 1,147.4 5.0 Bending 57.3 211.7 854 MTD10 LGGAVVAAPVAAAVAP 16 1,333.5 5.5 Bending 47.9 146.6 858 MTD73 PVLLLLA  7   737.9 6.0 No 36.1 278.5 -Bending 859 MTD77 AVALLILAV  9   882.1 5.6 No 30.3 271.1 -Bending 861 MTD85 LLAAAAALLLA 11 1,010.2 5.5 No   9.1* 231.8 -Bending 863 MTD103 LALPVLLLA  9   922.2 5.5 Bending 51.7 271.1 864 MTD132 AVVVPAIVLAAP 12 1,119.4 5.6 Bending 50.3 195.0 AVE 11 ± 3.2 1,083 ± 252 5.6 ± 0.1 Proline 41 ± 15 227 ± 47 Presence SEQ ID Hydropathy Residue A/a Composition Secondary NOs (GRAVY) Structure A V L I P G Structure Cargo Ref. 852 2.4 Aliphatic Ring 6 2 6 0 2 0 Helix p50 1 853 2.3 — 4 2 4 0 2 0 No-Helix CRE 2 854 1.8 — 7 4 1 0 2 2 Helix Parkin 8 858 2.8 — 1 1 4 0 1 0 Helix ES 6 859 3.3 — 3 2 3 1 0 0 Helix NM23 3 861 2.7 — 0 0 5 0 0 0 No-Helix RUHX3 5 863 2.8 — 2 1 5 0 1 0 Helix p18 4 864 2.4 — 4 4 1 1 2 0 No-Helix LIN28 7 AVE 2.5 ± 0.4 *Removing the MTD65 increases II to 45.6 ± 9.3.

Table 6 shows summarized Critical Factors of published hydrophobic Cell-Penetrating Peptides (B).

TABLE 6 Length: 11 ± 3.2 Molecular Weight: 1,083 ± 252 pI: 5.6 ± 0.1 Bending Potential (BP): Proline presences in the middle and/or the end of peptides, or No Proline. Instability Index (II): 41.0 ± 15 (^(▪) Removing the MTD85 increases II to 45.6 ± 9.3) Residue Structure & Aliphatic Index (AI): 227 ± 47 Hydropathy (GRAVY): 2.5 ± 0.4 Aliphatic Ring: Non-polar hydrophobic & aliphatic amino acid (A, V, L, I). Secondary Structure: α-Helix is favored but not required.

2-2. Selective Analysis (C) of Peptides that Provided Bending Potential and Higher Flexibility

To optimize the ‘Common Range and/or Consensus Feature of Critical Factor’ for the practical design of aMTDs and the random peptides (rPs or rPeptides), which were to prove that the ‘Critical Factors’ determined in the analysis A, B and C were correct to improve the current problems of hydrophobic CPPs—protein aggregation, low solubility/yield, and poor cell-/tissue-permeability of the recombinant proteins fused to the MTS/MTM or MTD, and non-common sequence and non-homologous structure of the peptides, empirically selected peptides were analyzed for their structural features and physicochemical factor indexes.

Hydrophobic CPPs which did not have a bending potential, rigid or too much flexible sequences (too much low or too much high Instability Index), or too low or too high hydrophobic CPPs were unselected, but secondary structure was not considered because helix structure of sequence was not required.

In analysis C, eight selected CPP sequences that could provide a bending potential and higher flexibility were finally analyzed (Table 7 and 8). Common amino acid length is 12 (11.6±3.0). Proline is presence in the middle of and/or the end of sequence. Rigidity/Flexibility (II) is 45.5-57.3 (Avg: 50.1±3.6). AI and GRAVY representing structural feature and hydrophobicity of the peptide are 204.7±37.5 and 2.4±0.3, respectively. All peptides are consisted with hydrophobic and aliphatic amino acids (A, V, L, I, and P). Therefore, analysis C was chosen as a standard for the new design of new hydrophobic CPPs—aMTDs.

Table 7 shows characteristics of published hydrophobic Cell-Penetrating Peptides (C): selected CPPs that provided bending potential and higher flexibility.

TABLE 7 Rigidity/ Structural SEQ Mole- Flexibility Feature ID cular Bending (Instability (Aliphatic NOS Peptide Sequence Length Weight pI Potential Index: II) Index: AI) 852 MTM AAVALLPAVLLALLAP 16 1515.9 5.6 Bending 45.5 220.0 853 MTS AAVLLPVLLAAP 12 1147.4 5.6 Bending 57.3 211.7 854 MTD10 LGGAVVAAPVAAAVAP 16 1333.5 5.5 Bending 47.9 140.6 856 MTD47 AAAVPVLVAA 10  881.0 5.6 Bending 47.5 176.0 858 MTD103 LALPVLLLA  9  922.2 5.5 Bending 51.7 271.1 864 MTD132 AVVVPAIVLAAP 12 1119.4 5.6 Bending 50.3 195.0 868 MTD173 AVIPILAVP  9  892.1 5.6 Bending 48.5 216.7 848 MTD161 AVLLLPAAA  9  838.0 5.6 Bending 51.7 206.7 AVE 11.6 ±   1081.2 ± 5.6 ± Proline   50.1 ±   204.7 ± 3.0  244.6 0.1 Presence  3.6  37.5 SEQ Hydro- A/a ID pathy Composition Secondary NOS (GRAVY) Residue Structure A V L I P G Structure Cargo Ref. 852 2.4 Aliphatic Ring 6 2 6 0 2 0 Helix p50 1 853 2.3 Aliphatic Ring 4 2 4 0 2 0 No-Helix CRE 2 854 1.8 Aliphatic Ring 7 4 1 0 2 2 Helix Parkin 8 856 2.4 Aliphatic Ring 5 3 1 0 1 0 No-Helix CMYC 4 858 2.8 Aliphatic Ring 2 1 5 0 1 0 Helix p18 8 864 2.4 Aliphatic Ring 4 4 1 1 2 0 No-Helix LIN28 4 868 2.4 Aliphatic Ring 2 2 1 2 2 0 Helix KLF4 4 848 2.4 Aliphatic Ring 4 1 3 0 1 0 No-Helix SOX2 4 AVE   2.4 ± Aliphatic Ring 0.3

Table 8 shows summarized Critical Factors of published hydrophobic Cell-Penetrating Peptides (C)

TABLE 8 Length: 11.6 ± 3.0 Molecular Weight: 1,081.2 ± 224.6 pI: 5.6 ± 0.1 Bending Potential (BP): Proline presences in the middle and/or the end of peptides. Instability Index (II): 50.1 ± 3.6 Residue Structure & Aliphatic Index (AI): 204.7 ± 37.5 Hydropathy (GRAVY): 2.4 ± 0.3 Aliphatic Ring: Non-polar hydrophobic & aliphatic amino acid (A, V, L, I). Secondary Structure: α-Helix is favored but not required. 3. New Design of Improved Hydrophobic CPPs—aMTDs Based on the Optimized Critical Factors

3-1. Determination of Common Sequence and/or Common Homologous Structure

As mentioned above, H-regions of signal sequence (HRSS)-derived CPPs (MTS/MTM and MTD) do not have a common sequence, sequence motif, and/or common-structural homologous feature. In this invention, the aim is to develop improved hydrophobic CPPs formatted in the common sequence- and structural-motif which satisfy newly determined ‘Critical Factors’ to have ‘Common Function,’ namely, to facilitate protein translocation across the membrane with similar mechanism to the analyzed reference CPPs. Based on the analysis A, B and C, the common homologous features have been analyzed to determine the critical factors that influence the cell-permeability. The range value of each critical factor has been determined to include the analyzed index of each critical factor from analysis A, B and C to design novel aMTDs (Table 9). These features have been confirmed experimentally with newly designed aMTDs in their cell-permeability.

Table 9 shows comparison the range/feature of each Critical Factor between the value of analyzed CPPs and the value determined for new design of novel aMTDs sequences

TABLE 9 Summarized Critical Factors of aMTD Selected CPPs Newly Designed CPPs Critical Factor Range Range Bending Potential Proline presences Proline presences (Proline Position: PP) in the middle in the middle and/or at the (5′, 6′, 7′ end of peptides or 8′) and at the end of peptides Rigidity/Flexibility 45.5-57.3 40-60 (Instability Index: II) (50.1 ± 3.6) Structural Feature 140.6-220.0 180-220 (Aliphatic Index: AI) (204.7 ± 37.5) Hydropathy 1.8-2.8 2.1-2.6 (Grand Average of  (2.4 ± 0.3) Hydropathy GRAVY) Length 11.6 ± 3.0  9-13 (Number of Amino Acid) Amino acid Composition A, V, I, L, P A, V, I, L, P

In Table 9, universal common features and sequence/structural motif are provided. Length is 9-13 amino acids, and bending potential is provided with the presence of proline in the middle of sequence (at 5′, 6′, 7′ or 8′ amino acid) for peptide bending and at the end of peptide for recombinant protein bending and Rigidity/Flexibility of aMTDs is II >40 are described in Table 9.

3-2. Critical Factors for Development of Advanced MTDs

Recombinant cell-permeable proteins fused to the hydrophobic CPPs to deliver therapeutically active cargo molecules including proteins into live cells had previously been reported, but the fusion proteins expressed in bacteria system were hard to be purified as a soluble form due to their low solubility and yield. To address the crucial weakness for further clinical development of the cell-permeable proteins as protein-based biotherapeutics, greatly improved form of the hydrophobic CPP, named as advanced MTD (aMTD) has newly been developed through critical factors-based peptide analysis. The critical factors used for the current invention of the aMTDs are herein (Table 9).

1. Amino Acid Length: 9-13

2. Bending Potential (Proline Position: PP)

: Proline presences in the middle (from 5′ to 8′ amino acid) and at the end of sequence

3. Rigidity/Flexibility (Instability Index: II): 40-60

4. Structural Feature (Aliphatic Index: AI): 180-220

5. Hydropathy (GRAVY): 2.1-2.6

6. Amino Acid Composition: Hydrophobic and Aliphatic amino acids—A, V, L, I and P

3-3. Design of Potentially Best aMTDs that all Critical Factors are Considered and Satisfied

After careful consideration of six critical factors derived from analysis of unique features of hydrophobic CPPs, advanced macromolecule transduction domains (aMTDs) have been designed and developed based on the common 12 amino acid platform which satisfies the critical factors including amino acid length (9-13) determined from the analysis.

Unlike previously published hydrophobic CPPs that require numerous experiments to determine their cell-permeability, newly developed aMTD sequences could be designed by performing just few steps as follows using above mentioned platform to follow the determined range value/feature of each critical factor.

First, prepare the 12 amino acid sequence platform for aMTD. Second, place proline (P) in the end (12′) of sequence and determine where to place proline in one of four U(s) in 5′, 6′, 7′, and 8. Third, alanine (A), valine (V), leucine (L) or isoleucine (I) is placed in either X(s) and/or U(s), where proline is not placed. Lastly, determine whether the amino acid sequences designed based on the platform, satisfy the value or feature of six critical factors to assure the cell permeable property of aMTD sequences. Through these processes, numerous novel aMTD sequences have been constructed. The expression vectors for preparing non-functional cargo recombinant proteins fused to each aMTD, expression vectors have been constructed and forcedly expressed in bacterial cells. These aMTD-fused recombinant proteins have been purified in soluble form and determined their cell-permeability quantitatively. aMTD sequences have been newly designed, numbered from 1 to 240, as shown in Table 10-15. In Table 10-15, sequence ID Number is a sequence listings for reference, and aMTD numbers refer to amino acid listing numbers that actually have been used at the experiments. For further experiments, aMTD numbers have been used. In addition, polynucleotide sequences shown in the sequence lists have been numbered from SEQ ID NO: 241 to SEQ ID NO: 480.

Tables 10 to 15 shows 240 new hydrophobic aMTD sequences that were developed to satisfy all critical factors.

TABLE 10 Rigidity/ Structural Sequence Flexibility Feature Hydropathy Residue ID Number aMTD Sequences Length (II) (AI) (GRAVY) Structure  1  1 AAALAPVVLALP 12 57.3 187.5 2.1 Aliphatic  2  2 AAAVPLLAVVVP 12 41.3 195.0 2.4 Aliphatic  3  3 AALLVPAAVLAP 12 57.3 187.5 2.1 Aliphatic  4  4 ALALLPVAALAP 12 57.3 195.8 2.1 Aliphatic  5  5 AAALLPVALVAP 12 57.3 187.5 2.1 Aliphatic  6 11 VVALAPALAALP 12 57.3 187.5 2.1 Aliphatic  7 12 LLAAVPAVLLAP 12 57.3 211.7 2.3 Aliphatic  8 13 AAALVPVVALLP 12 57.3 203.3 2.3 Aliphatic  9 21 AVALLPALLAVP 12 57.3 211.7 2.3 Aliphatic 10 22 AVVLVPVLAAAP 12 57.3 195.0 2.4 Aliphatic 11 23 VVLVLPAAAAVP 12 57.3 195.0 2.4 Aliphatic 12 24 IALAAPALIVAP 12 50.2 195.8 2.2 Aliphatic 13 25 IVAVAPALVALP 12 50.2 203.3 2.4 Aliphatic 14 42 VAALPVVAVVAP 12 57.3 196.7 2.4 Aliphatic 15 43 LLAAPLVVAAVP 12 41.3 187.5 2.1 Aliphatic 16 44 ALAVPVALLVAP 12 57.3 203.3 2.3 Aliphatic 17 61 VAALPVLLAALP 12 57.3 211.7 2.3 Aliphatic 18 62 VALLAPVALAVP 12 57.3 203.3 2.3 Aliphatic 19 63 AALLVPALVAVP 12 57.3 203.3 2.3 Aliphatic

TABLE 11 Rigidity/ Structural Sequence Flexibility Feature Hydropathy Residue ID Number aMTD Sequences Length (II) (AI) (GRAVY) Structure 20  64 AIVALPVAVLAP 12 50.2 203.3 2.4 Aliphatic 21  65 IAIVAPVVALAP 12 50.2 203.3 2.4 Aliphatic 22  81 AALLPALAALLP 12 57.3 204.2 2.1 Aliphatic 23  82 AVVLAPVAAVLP 12 57.3 195.0 2.4 Aliphatic 24  83 LAVAAPLALALP 12 41.3 195.8 2.1 Aliphatic 25  84 AAVAAPLLLALP 12 41.3 195.8 2.1 Aliphatic 26 85 LLVLPAAALAAP 12 57.3 195.8 2.1 Aliphatic 27 101 LVALAPVAAVLP 12 57.3 203.3 2.3 Aliphatic 28 102 LALAPAALALLP 12 57.3 204.2 2.1 Aliphatic 29 103 ALIAAPILALAP 12 57.3 204.2 2.2 Aliphatic 30 104 AVVAAPLVLALP 12 41.3 203.2 2.3 Aliphatic 31 105 LLALAPAALLAP 12 57.3 204.1 2.1 Aliphatic 32 121 AIVALPALALAP 12 50.2 195.8 2.2 Aliphatic 33 123 AAIIVPAALLAP 12 50.2 195.8 2.2 Aliphatic 34 124 IAVALPALIAAP 12 50.3 195.8 2.2 Aliphatic 35 141 AVIVLPALAVAP 12 50.2 203.3 2.4 Aliphatic 36 143 AVLAVPAVLVAP 12 57.3 195.0 2.4 Aliphatic 37 144 VLAIVPAVALAP 12 50.2 203.3 2.4 Aliphatic 38 145 LLAVVPAVALAP 12 57.3 203.3 2.3 Aliphatic 39 161 AVIALPALIAAP 12 57.3 195.8 2.2 Aliphatic 40 162 AVVALPAALIVP 12 50.2 203.3 2.4 Aliphatic 41 163 LALVLPAALAAP 12 57.3 195.8 2.1 Aliphatic 42 164 LAAVLPALLAAP 12 57.3 195.8 2.1 Aliphatic 43 165 ALAVPVALAIVP 12 50.2 203.3 2.4 Aliphatic 44 182 ALIAPVVALVAP 12 57.3 203.3 2.4 Aliphatic 45 183 LLAAPVVIALAP 12 57.3 211.6 2.4 Aliphatic 46 184 LAAIVPAIIAVP 12 50.2 211.6 2.4 Aliphatic 47 185 AALVLPLIIAAP 12 41.3 220.0 2.4 Aliphatic 48 201 LALAVPALAALP 12 57.3 195.8 2.1 Aliphatic 49 204 LIAALPAVAALP 12 57.3 195.8 2.2 Aliphatic 50 205 ALALVPAIAALP 12 57.3 195.8 2.2 Aliphatic 51 221 AAILAPIVALAP 12 50.2 195.8 2.2 Aliphatic 52 222 ALLIAPAAVIAP 12 57.3 195.8 2.2 Aliphatic 53 223 AILAVPIAVVAP 12 57.3 203.3 2.4 Aliphatic 54 224 ILAAVPIALAAP 12 57.3 195.8 2.2 Aliphatic 55 225 VAALLPAAAVLP 12 57.3 187.5 2.1 Aliphatic 56 241 AAAVVPVLLVAP 12 57.3 195.0 2.4 Aliphatic 57 242 AALLVPALVAAP 12 57.3 187.5 2.1 Aliphatic 58 243 AAVLLPVALAAP 12 57.3 187.5 2.1 Aliphatic 59 245 AAALAPVLALVP 12 57.3 187.5 2.1 Aliphatic 60 261 LVLVPLLAAAAP 12 41.3 211.6 2.3 Aliphatic 61 262 ALIAVPAIIVAP 12 50.2 211.6 2.4 Aliphatic 62 263 ALAVIPAAAILP 12 54.9 195.8 2.2 Aliphatic 63 264 LAAAPVVIVIAP 12 50.2 203.3 2.4 Aliphatic 64 265 VLAIAPLLAAVP 12 41.3 211.6 2.3 Aliphatic 65 281 ALIVLPAAVAVP 12 50.2 203.3 2.4 Aliphatic 66 282 VLAVAPALIVAP 12 50.2 203.3 2.4 Aliphatic 67 283 AALLAPALIVAP 12 50.2 195.8 2.2 Aliphatic 68 284 ALIAPAVALIVP 12 50.2 211.7 2.4 Aliphatic 69 285 AIVLLPAAVVAP 12 50.2 203.3 2.4 Aliphatic

TABLE 12 Rigidity/ Structural Sequence Flexibility Feature Hydropathy Residue ID Number aMTD Sequences Length (II) (AI) (GRAVY) Structure  70 301 VIAAPVLAVLAP 12 57.3 203.3 2.4 Aliphatic  71 302 LALAPALAILAP 12 57.3 204.2 2.1 Aliphatic  72 304 AIILAPIAAIAP 12 57.3 204.2 2.3 Aliphatic  73 305 IALAAPILLAAP 12 57.3 204.2 2.2 Aliphatic  74 321 IVAVALPALAVP 12 50.2 203.3 2.3 Aliphatic  75 322 VVAIVLPALAAP 12 50.2 203.3 2.3 Aliphatic  76 323 IVAVALPVALAP 12 50.2 203.3 2.3 Aliphatic  77 324 IVAVALPAALVP 12 50.2 203.3 2.3 Aliphatic  78 325 IVAVALPAVALP 12 50.2 203.3 2.3 Aliphatic  79 341 IVAVALPAVLAP 12 50.2 203.3 2.3 Aliphatic  80 342 VIVALAPAVLAP 12 50.2 203.3 2.3 Aliphatic  81 343 IVAVALPALVAP 12 50.2 203.3 2.3 Aliphatic  82 345 ALLIVAPVAVAP 12 50.2 203.3 2.3 Aliphatic  83 361 AVVIVAPAVIAP 12 50.2 195.0 2.4 Aliphatic  84 363 AVLAVAPALIVP 12 50.2 203.3 2.3 Aliphatic  85 364 LVAAVAPALIVP 12 50.2 203.3 2.3 Aliphatic  86 365 AVIVVAPALLAP 12 50.2 203.3 2.3 Aliphatic  87 381 VVAIVLPAVAAP 12 50.2 195.0 2.4 Aliphatic  88 382 AAALVIPAILAP 12 54.9 195.8 2.2 Aliphatic  89 383 VIVALAPALLAP 12 50.2 211.6 2.3 Aliphatic  90 384 VIVAIAPALLAP 12 50.2 211.6 2.4 Aliphatic  91 385 IVAIAVPALVAP 12 50.2 203.3 2.4 Aliphatic  92 401 AALAVIPAAILP 12 54.9 195.8 2.2 Aliphatic  93 402 ALAAVIPAAILP 12 54.9 195.8 2.2 Aliphatic  94 403 AAALVIPAAILP 12 54.9 195.8 2.2 Aliphatic  95 404 LAAAVIPAAILP 12 54.9 195.8 2.2 Aliphatic  96 405 LAAAVIPVAILP 12 54.9 211.7 2.4 Aliphatic  97 421 AAILAAPLIAVP 12 57.3 195.8 2.2 Aliphatic  98 422 VVAILAPLLAAP 12 57.3 211.7 2.4 Aliphatic  99 424 AVVVAAPVLALP 12 57.3 195.0 2.4 Aliphatic 100 425 AVVAIAPVLALP 12 57.3 203.3 2.4 Aliphatic 101 442 ALAALVPAVLVP 12 57.3 203.3 2.3 Aliphatic 102 443 ALAALVPVALVP 12 57.3 203.3 2.2 Aliphatic 103 444 LAAALVPVALVP 12 57.3 203.3 2.3 Aliphatic 104 445 ALAALVPALVVP 12 57.3 203.3 2.2 Aliphatic 105 461 IAAVIVPAVALP 12 50.2 203.3 2.4 Aliphatic 106 462 IAAVLVPAVALP 12 57.3 203.3 2.4 Aliphatic 107 463 AVAILVPLLAAP 12 57.3 211.7 2.4 Aliphatic 108 464 AVVILVPLAAAP 12 57.3 203.3 2.4 Aliphatic 109 465 IAAVIVPVAALP 12 50.2 203.3 2.4 Aliphatic 110 481 AlAIAIVPVALP 12 50.2 211.6 2.4 Aliphatic 111 482 ILAVAAIPVAVP 12 54.9 203.3 2.4 Aliphatic 112 483 ILAAAIIPAALP 12 54.9 204.1 2.2 Aliphatic 113 484 LAVVLAAPAIVP 12 50.2 203.3 2.4 Aliphatic 114 485 AILAAIVPLAVP 12 50.2 211.6 2.4 Aliphatic 115 501 VIVALAVPALAP 12 50.2 203.3 2.4 Aliphatic 116 502 AIVALAVPVLAP 12 50.2 203.3 2.4 Aliphatic 117 503 AAIIIVLPAALP 12 50.2 220.0 2.4 Aliphatic 118 504 LIVALAVPALAP 12 50.2 211.7 2.4 Aliphatic 119 505 AIIIVIAPAAAP 12 50.2 195.8 2.3 Aliphatic

TABLE 13 Rigidity/ Structural Sequence Flexibility Feature Hydropathy Residue ID Number aMTD Sequences Length (II) (AI) (GRAVY) Structure 120 521 LAALIVVPAVAP 12 50.2 203.3 2.4 Aliphatic 121 522 ALLVIAVPAVAP 12 57.3 203.3 2.4 Aliphatic 122 524 AVALIVVPALAP 12 50.2 203.3 2.4 Aliphatic 123 525 ALAIVVAPVAVP 12 50.2 195.0 2.4 Aliphatic 124 541 LLALIIAPAAAP 12 57.3 204.1 2.1 Aliphatic 125 542 ALALIIVPAVAP 12 50.2 211.6 2.4 Aliphatic 126 543 LLAAL1APAALP 12 57.3 204.1 2.1 Aliphatic 127 544 IVALIVAPAAVP 12 43.1 203.3 2.4 Aliphatic 128 545 VVLVLAAPAAVP 12 57.3 195.0 2.3 Aliphatic 129 561 AAVAIVLPAVVP 12 50.2 195.0 2.4 Aliphatic 130 562 ALIAAIVPALVP 12 50.2 211.7 2.4 Aliphatic 131 563 ALAVIVVPALAP 12 50.2 203.3 2.4 Aliphatic 132 564 VAIALIVPALAP 12 50.2 211.7 2.4 Aliphatic 133 565 VAIVLVAPAVAP 12 50.2 195.0 2.4 Aliphatic 134 582 VAVALIVPALAP 12 50.2 203.3 2.4 Aliphatic 135 583 AVILALAPIVAP 12 50.2 211.6 2.4 Aliphatic 136 585 ALIVAIAPALVP 12 50.2 211.6 2.4 Aliphatic 137 601 AAILIAVPIAAP 12 57.3 195.8 2.3 Aliphatic 138 602 VIVALAAPVLAP 12 50.2 203.3 2.4 Aliphatic 139 603 VLVALAAPVIAP 12 57.3 203.3 2.4 Aliphatic 140 604 VALIAVAPAVVP 12 57.3 195.0 2.4 Aliphatic 141 605 VIAAVLAPVAVP 12 57.3 195.0 2.4 Aliphatic 142 622 ALIVLAAPVAVP 12 50.2 203.3 2.4 Aliphatic 143 623 VAAAIALPAIVP 12 50.2 187.5 2.3 Aliphatic 144 625 ILAAAAAPLIVP 12 50.2 195.8 2.2 Aliphatic 145 643 LALVLAAPAIVP 12 50.2 211.6 2.4 Aliphatic 146 645 ALAVVALPAIVP 12 50.2 203.3 2.4 Aliphatic 147 661 AAILAPIVAALP 12 50.2 195.8 2.2 Aliphatic 148 664 ILIAIAIPAAAP 12 54.9 204.1 2.3 Aliphatic 149 665 LAIVLAAPVAVP 12 50.2 203.3 2.3 Aliphatic 150 666 AAIAIIAPAIVP 12 50.2 195.8 2.3 Aliphatic 151 667 LAVAIVAPALVP 12 50.2 203.3 2.3 Aliphatic 152 683 LAIVLAAPAVLP 12 50.2 211.7 2.4 Aliphatic 153 684 AAIVLALPAVLP 12 50.2 211.7 2.4 Aliphatic 154 685 ALLVAVLPAALP 12 57.3 211.7 2.3 Aliphatic 155 686 AALVAVLPVALP 12 57.3 203.3 2.3 Aliphatic 156 687 AILAVALPLLAP 12 57.3 220.0 2.3 Aliphatic 157 703 IVAVALVPALAP 12 50.2 203.3 2.4 Aliphatic 158 705 IVAVALLPAIAP 12 50.2 211.7 2.4 Aliphatic 159 706 IVAVALLPAVAP 12 50.2 203.3 2.4 Aliphatic 160 707 IVALAVLPAVAP 12 50.2 203.3 2.4 Aliphatic 161 724 VAVLAVLPALAP 12 57.3 203.3 2.3 Aliphatic 162 726 IAVLAVAPAVLP 12 57.3 203.3 2.3 Aliphatic 163 726 LAVAIIAPAVAP 12 57.3 187.5 2.2 Aliphatic 164 727 VALAIALPAVIP 12 57.3 211.6 2.3 Aliphatic 165 743 AIAIALVPVALP 12 57.3 211.6 2.4 Aliphatic 166 744 AAVVIVAPVALP 12 50.2 195.0 2.4 Aliphatic 167 746 VAIIVVAPALAP 12 50.2 203.3 2.4 Aliphatic 168 747 VALLAIAPALAP 12 57.3 195.8 2.2 Aliphatic 169 763 VAVLIAVPAIAP 12 57.3 203.3 2.3 Aliphatic

TABLE 14 Rigidity/ Structural Sequence Flexibility Feature Hydropathy Residue ID Number aMTD Sequences Length (II) (AI) (GRAVY) Structure 170 764 AVALAVLPAVVP 12 57.3 195.0 2.3 Aliphatic 171 765 AVALAVVPAVLP 12 57.3 195.0 2.3 Aliphatic 172 766 IVVIAVAPAVAP 12 50.2 195.0 2.4 Aliphatic 173 767 IVVAAVVPALAP 12 50.2 195.0 2.4 Aliphatic 174 783 IVALVPAVAIAP 12 50.2 203.3 2.5 Aliphatic 175 784 VAALPAVALVVP 12 57.3 195.0 2.4 Aliphatic 176 786 IVAIAPLAVLAP 12 41.3 211.7 2.4 Aliphatic 177 787 AVALVPVIVAAP 12 50.2 195.0 2.4 Aliphatic 178 788 AIAVAIAPVALP 12 57.3 187.5 2.3 Aliphatic 179 803 AIALAVPVLALP 12 57.3 211.7 2.4 Aliphatic 180 805 LVLIAAAPIALP 12 41.3 220.0 2.4 Aliphatic 181 806 LVALAVPAAVLP 12 57.3 203.3 2.3 Aliphatic 182 807 AVALAVPALVLP 12 57.3 203.3 2.3 Aliphatic 183 808 LVVLAAAPLAVP 12 41.3 203.3 2.2 Aliphatic 184 809 LIVLAAPALAAP 12 50.2 195.8 2.2 Aliphatic 185 810 VIVLAAPALAAP 12 50.2 187.5 2.2 Aliphatic 186 811 AVVLAVPALAVP 12 57.3 195.0 2.3 Aliphatic 187 824 LIIVAAAPAVAP 12 50.2 187.5 2.3 Aliphatic 188 825 IVAVIVAPAVAP 12 43.2 195.0 2.5 Aliphatic 189 826 LVALAAPIIAVP 12 41.3 211.7 2.4 Aliphatic 190 827 IAAVLAAPALVP 12 57.3 187.5 2.2 Aliphatic 191 828 IALLAAPIIAVP 12 41.3 220.0 2.4 Aliphatic 192 829 AALALVAPVIVP 12 50.2 203.3 2.4 Aliphatic 193 830 IALVAAPVALVP 12 57.3 203.3 2.4 Aliphatic 194 831 IIVAVAPAAIVP 12 43.2 203.3 2.5 Aliphatic 195 832 AVAAIVPVIVAP 12 43.2 195.0 2.5 Aliphatic 196 843 AVLVLVAPAAAP 12 41.2 219.2 2.5 Aliphatic 197 844 VVALLAPLIAAP 12 41.3 211.8 2.4 Aliphatic 198 845 AAVVIAPLLAVP 12 41.2 203.3 2.4 Aliphatic 199 846 IAVAVAAPLLVP 12 41.3 203.3 2.4 Aliphatic 200 847 LVAIVVLPAVAP 12 50.2 219.2 2.6 Aliphatic 201 848 AVAIVVLPAVAP 12 50.2 195.0 2.4 Aliphatic 202 849 AVILLAPLIAAP 12 57.3 220.0 2.4 Aliphatic 203 850 LVIALAAPVALP 12 57.3 211.7 2.4 Aliphatic 204 851 VLAVVLPAVALP 12 57.3 219.2 2.5 Aliphatic 205 852 VLAVAAPAVLLP 12 57.3 203.3 2.3 Aliphatic 206 863 AAVVLLPIIAAP 12 41.3 211.7 2.4 Aliphatic 207 864 ALLVIAPAIAVP 12 57.3 211.7 2.4 Aliphatic 208 865 AVLVIAVPAIAP 12 57.3 203.3 2.5 Aliphatic 209 867 ALLVVIAPLAAP 12 41.3 211.7 2.4 Aliphatic 210 868 VLVAAILPAAIP 12 54.9 211.7 2.4 Aliphatic 211 870 VLVAAVLPIAAP 12 41.3 203.3 2.4 Aliphatic 212 872 VLAAAVLPLVVP 12 41.3 219.2 2.5 Aliphatic 213 875 AIAIVVPAVAVP 12 50.2 195.0 2.4 Aliphatic 214 877 VAIIAVPAVVAP 12 57.3 195.0 2.4 Aliphatic 215 878 IVALVAPAAVVP 12 50.2 195.0 2.4 Aliphatic 216 879 AAIVLLPAVVVP 12 50.2 219.1 2.5 Aliphatic 217 881 AALIVVPAVAVP 12 50.2 195.0 2.4 Aliphatic 218 882 AIALVVPAVAVP 12 57.3 195.0 2.4 Aliphatic 219 883 LAIVPAAIAALP 12 50.2 195.8 2.2 Aliphatic

TABLE 15 Rigidity/ Structural Sequence Flexibility Feature Hydropathy Residue ID Number aMTD Sequences Length (II) (AI) (GRAVY) Structure 220 885 LVAIAPAVAVLP 12 57.3 203.3 2.4 Aliphatic 221 887 VLAVAPAVAVLP 12 57.3 195.0 2.4 Aliphatic 222 888 ILAVVAIPAAAP 12 54.9 187.5 2.3 Aliphatic 223 889 ILVAAAPIAALP 12 57.3 195.8 2.2 Aliphatic 224 891 ILAVAAIPAALP 12 54.9 195.8 2.2 Aliphatic 225 893 VIAIPAILAAAP 12 54.9 195.8 2.3 Aliphatic 226 895 AIIIVVPAIAAP 12 50.2 211.7 2.5 Aliphatic 227 896 AILIVVAPIAAP 12 50.2 211.7 2.5 Aliphatic 228 897 AVIVPVAIIAAP 12 50.2 203.3 2.5 Aliphatic 229 899 AVVIALPAVVAP 12 57.3 195.0 2.4 Aliphatic 230 900 ALVAVIAPVVAP 12 57.3 195.0 2.4 Aliphatic 231 901 ALVAVIPAVAVP 12 57.3 195.0 2.4 Aliphatic 232 902 ALVAPLLAVAVP 12 41.3 203.3 2.3 Aliphatic 233 904 AVLAVVAPVVAP 12 57.3 186.7 2.4 Aliphatic 234 905 AVIAVAPLVVAP 12 41.3 195.0 2.4 Aliphatic 235 906 AVIALAPVVVAP 12 57.3 195.0 2.4 Aliphatic 236 907 VAIALAPVVVAP 12 57.3 195.0 2.4 Aliphatic 237 908 VALALAPVVVAP 12 57.3 195.0 2.3 Aliphatic 238 910 VAALLPAVVVAP 12 57.3 195.0 2.3 Aliphatic 239 911 VALALPAVVVAP 12 57.3 195.0 2.3 Aliphatic 240 912 VALLAPAVVVAP 12 57.3 195.0 2.3 Aliphatic 52.6 ± 5.1 201.7 ± 7.8 2.3 ± 0.1

3-4. Design of the Peptides that Did not Satisfy at Least One Critical Factor

To demonstrate that this invention of new hydrophobic CPPs—aMTDs, which satisfy all critical factors described above, are correct and rationally designed, the peptides which do not satisfy at least one critical factor have also been designed. Total of 31 rPeptides (rPs) are designed, developed and categorized as follows: no bending peptides, either no proline in the middle as well at the end and/or no central proline; rigid peptides (II<40); too much flexible peptides; aromatic peptides (aromatic ring presences); hydrophobic, with non-aromatic peptides but have amino acids other than A, V, L, I, P or additional proline residues; hydrophilic, but non-aliphatic peptides.

3-4-1. Peptides that do not Satisfy the Bending Potential

Table 16 shows the peptides that do not have any proline in the middle (at 5′, 6′, 7′ or 8′) and at the end of the sequences. In addition, Table 16 describes the peptides that do not have proline in the middle of the sequences. All these peptides are supposed to have no-bending potential.

TABLE 16 Proline Rigidity/ Sturctural rPeptide ID Position Flexibility Feature Hydropathy Group (SEQ ID No) Sequences Length (PP) (II) (AI) (GRAVY) No-Bending Peptides 931 (869) AVLIAPAILAAA 12 6 57.3 204.2 2.5 (No Proline at 5 or 6 936 (870) ALLILAAAVAAP 12 12 41.3 204.2 2.4 and/or 12) and 152 (71) LAAAVAAVAALL 12 None 9.2 204.2 2.7 (No Central Proline)  27 (872) LAIVAAAAALVA 12 None 2.1 204.2 2.8 935 (873) ALLILPAAAVAA 12 6 57.3 204.2 2.4 670 (874) ALLILAAAVAAL 12 None 25.2 236.6 2.8 934 (875) LILAPAAVVAAA 12 5 57.3 195.6 2.5  37 (876) TTCSQQQYCTNG 12 None 53.1 0 −1.1  16 (877) NNSCTTYTNGSQ 12 None 47.4 0 −1.4 113 (878) PVAVALLIAVPP 12 1, 11, 12 57.3 195 2.1

3-4-2. Peptides that do not Satisfy the Rigidity/Flexibility

To prove that rigidity/flexibility of the sequence is a crucial critical factor, rigid (Avg. II: 21.8±6.6) and too high flexible sequences (Avg. II: 82.3±21.0) were also designed. Rigid peptides that instability index is much lower than that of new aMTDs (II: 41.3-57.3, Avg. II: 53.3±5.7) are shown in Table 17. Bending, but too high flexible peptides that II is much higher than that of new aMTDs are also provided in Table 18.

TABLE 17 Proline Rigidity/ Sturctural rPeptide ID Position Flexibility Feature Hydropathy Group (SEQ ID No) Sequences Length (PP) (II) (AI) (GRAVY) Rigid 226 (879) ALVAAIPALAIP 12 6 20.4 195.8 2.2 Peptides   6 (880) VIAMIPAAFWVA 12 6 15.7 146.7 2.2 (II < 50) 750 (881) LAIAAIAPLAIP 12 8, 12 22.8 204.2 2.2  26 (882) AAIALAAPLAIV 12 8 18.1 204.2 2.5 527 (883) LVLAAVAPIAIP 12 8, 12 22.8 211.7 2.4 466 (884) IIAAAAPLAIIP 12 7, 12 22.8 204.2 2.3 167 (885) VAIAIPAALAIP 12 6, 12 20.4 195.8 2.3 246 (886) VVAVPLLVAFAA 12 5 25.2 195 2.7 426 (887) AAALAIPLAIIP 12 7, 12 4.37 204.2 2.2 606 (888) AAAIAAIPIIIP 12 8, 12 4.4 204.2 2.4  66 (889) AGVLGGPIMGVP 12 7, 12 35.5 121.7 1.3 248 (890) VAAIVPIAALVP 12 6, 12 34.2 203.3 2.5 227 (891) LAAIVPIAAAVP 12 6, 12 34.2 187.5 2.2  17 (892) GGCSAPQTTCSN 12 6 51.6 8.3 −0.5  67 (893) LDAEVPLADDVP 12 6, 12 34.2 130 0.3

TABLE 18 Proline Rigidity/ Sturctural rPeptide ID Position Flexibility Feature Hydropathy Group (SEQ ID No) Sequences Length (PP) (II) (AI) (GRAVY) Bending 692 (894) PAPLPPVVILAV 12 1, 3, 5, 6 105.5 186.7 1.8 Peptides,  69 (895) PVAVLPPAALVP 12 1, 5, 7, 12 89.4 162.5 1.6 but Too 390 (896) VPLLVPVVPVVP 12 2, 6, 9, 12 105.4 210 2.2 High 350 (897) VPILVPVVPVVP 12 2, 6, 9, 12 121.5 210 2.2 Flexibility 331 (898) VPVLVPLVPVVP 12 2, 6, 9, 12 105.4 210 2.2   9 (899) VALVPAALILPP 12 5, 11, 12 89.4 203.3 2.1  68 (900) VAPVLPAAPLVP 12 3, 6, 9, 12 105.5 162.5 1.6 349 (901) VPVLVPVVPVVP 12 2, 6, 9 ,12 121.5 201.6 2.2 937 (902) VPVLVPLPVPVV 12 2, 6, 8, 10 121.5 210 2.2 938 (903) VPVLLPVVVPVP 12 2, 6, 10,12 121.5 210 2.2 329 (904) LPVLVPVVPVVP 12 2, 6, 9, 12 121.5 210 2.2  49 (905) VVPAAPAVPVVP 12 3, 6, 9, 12 121.5 145.8 1.7 772 (906) LPVAPVIPIIVP 12 2, 5, 8, 12 79.9 210.8 2.1 210 (907) ALIALPALPALP 12 6, 9, 12 89.4 195.8 1.8  28 (908) AVPLLPLVPAVP 12 3, 6, 9, 12 89.4 186.8 1.8 693 (909) AAPVLPVAVPIV 12 3, 6, 10 82.3 186.7 2.1 169 (910) VALVAPALILAP 12 6, 12 73.4 211.7 2.4  29 (911) VLPPLPVLPVLP 12 3, 4, 6, 9, 12 121.5 202.5 1.7 190 (912) AAILAPAVIAPP 12 6, 11, 12 89.4 163.3 1.8

3-4-3. Peptides that do not Satisfy the Structural Features

New hydrophobic CPPs—aMTDs are consisted with only hydrophobic and aliphatic amino acids (A, V, L, I and P) with average ranges of the indexes—AI: 180-220 and GRAVY: 2.1-2.6 (Table 9). Based on the structural indexes, the peptides which contain an aromatic residue (W, F or Y) are shown in Table 19 and the peptides which are hydrophobic with non-aromatic sequences but have amino acids residue other than A, V, L, I, P or additional proline residues are designed (Table 20). Finally, hydrophilic and/or bending peptides which are consisted with non-aliphatic amino acids are shown in Table 21.

TABLE 19 Proline Rigidity/ Sturctural rPeptide ID Position Flexibility Feature Hydropathy Group (SEQ ID No) Sequences Length (PP) (II) (AI) (GRAVY) Aromatic  30 (913) AMALLPAAVAVA 12 6 51.6 163.3 2.3 Peptides  33 (914) AAAILAPAFLAV 12 7 57.3 171.7 2.4 (Aromatic 131 (915) WIIAPVWLAWIA 12 5 51.6 179.2 1.9 Ring 922 (916) WYVIFVLPLVVP 12 8, 12 41.3 194.2 2.2 Presences)  71 (917) FMWMWFPFMWYP 12 7, 12 71.3 0 0.6 921 (918) IWWFWVVPLVVP 12 8, 12 41.3 194.2 2.2

TABLE 20 Proline Rigidity/ Sturctural rPeptide ID Position Flexibility Feature Hydropathy Group (SEQ ID No) Sequences Length (PP) (II) (AI) (GRAVY) Hydrophobic 436 (919) VVMLVVPAVMLP 12 7, 12 57.3 194.2 2.6 but Non 138 (920) PPAALLAILAVA 12 1, 2 57.3 195.8 2.2 Aromatic  77 (921) PVALVIVALVAP 12 1, 12 41.3 219.2 2.5 Peptides 577 (922) MLMIALVPMIAV 12 8 18.9 195 2.7  97 (923) ALLAAPPALLAL 12 6, 7 57.3 204.2 2.1 214 (924) ALIVAPALMALP 12 6, 12 60.5 187.5 2.2  59 (925) AVLAAPVVAALA 12 6 41.3 187.5 2.5  54 (926) LAVAAPPVVALL 12 6, 7 57.3 203.3 2.3

TABLE 21 Proline Rigidity/ Sturctural rPeptide ID Position Flexibility Feature Hydropathy Group (SEQ ID No) Sequences Length (PP) (II) (AI) (GRAVY) Hydrophilic 949 (927) SGNSCQQCGNSS 12 None 41.7 0 −1.1 Peptides  39 (928) CYNTSPCTGCCY 12 6 52.5 0 0 but Non  19 (929) YVSCCTYTNGSQ 12 None 47.7 0 −1 Aliphatic 947 (930) CYYNQQSNNNNQ 12 None 59.6 0 −2.4 139 (931) TGSTNSPTCTST 12 7 53.4 0 −0.7  18 (932) NVCCTPTTNGQS 12 6 47.9 0 −0.9  20 (933) NYCNTCPTYGQS 12 7 47.4 0 −0.9 635 (934) GSTGGSQQNNQY 12 None 31.9 0 −1.9  40 (935) TYNTSCTPGTCY 12 8 49.4 0.0 −0.6  57 (936) QNNCNTSSQGGG 12 None 52.4 0 −1.6 159 (937) CYSGSTSQNQPP 12 11, 12 51 0 −1.3 700 (938) GTSNTCQSNQNS 12 None 19.1 0 −1.6  38 (939) YYNQSTCGGQCY 12 None 53.8 0 −1

3-5. Summary of Newly Designed Peptides

Total of 457 sequences have been designed based on the critical factors. Designed potentially best aMTDs (hydrophobic, flexible, bending, aliphatic and 12-A/a length peptides) that do satisfy all range/feature of critical factors are 316. Designed rPeptides that do not satisfy at least one of the critical factors are 141 that no bending peptide sequences are 26; rigid peptide (II<40) sequences are 23; too much flexible peptides are 24; aromatic peptides (aromatic ring presences) are 27; hydrophobic, but non-aromatic peptides are 23; and hydrophilic, but non-aliphatic peptides are 18.

4. Preparation of Recombinant Report Proteins Fused to aMTDs and rPeptides

Recombinant proteins fused to aMTDs and others [rPeptides, reference hydrophobic CPP sequences (MTM and MTD)] were expressed in a bacterial system, purified with single-step affinity chromatography and prepared as soluble proteins in physiological condition. These recombinant proteins have been tested for the ability of their cell-permeability by utilizing flow cytometry and laser scanning confocal microscopy.

4-1. Selection of Cargo Protein for Recombinant Proteins Fused to Peptide Sequences

For clinical/non-clinical application, aMTD-fused cargo materials would be biologically active molecules that could be one of the following: enzymes, transcription factors, toxic, antigenic peptides, antibodies and antibody fragments. Furthermore, biologically active molecules could be one of these following macromolecules: enzymes, hormones, carriers, immunoglobulin, membrane-bound proteins, transmembrane proteins, internal proteins, external proteins, secreted proteins, virus proteins, native proteins, glycoproteins, fragmented proteins, disulfide bonded proteins, recombinant proteins, chemically modified proteins and prions. In addition, these biologically active molecules could be one of the following: nucleic acid, coding nucleic acid sequence, mRNAs, antisense RNA molecule, carbohydrate, lipid and glycolipid.

According to these pre-required conditions, a non-functional cargo to evaluate aMTD-mediated protein uptake has been selected and called as Cargo A (CRA) that should be soluble and non-functional. The domain (A/a 289-840; 184 A/a length) is derived from protein S (Genbank ID: CP000113.1).

4-2. Construction of Expression Vector and Preparation of Recombinant Proteins

Coding sequences for recombinant proteins fused to each aMTD are cloned Nde1 (5′) and SalI (3′) in pET-28a(+) (Novagen, Darmstadt, Germany) from PCR-amplified DNA segments. PCR primers for the recombinant proteins fused to aMTD and rPeptides are SEQ ID NOs: 481˜797. Structure of the recombinant proteins is displayed in FIG. 1.

The recombinant proteins were forcedly expressed in E. coli BL21 (DE3) cells grown to an OD₆₀₀ of 0.6 and induced for 2 hours with 0.7 mM isopropyl-β-D-thiogalactopyranoside (IPTG). The proteins were purified by Ni²⁺ affinity chromatography as directed by the supplier (Qiagen, Hilden, Germany) in natural condition. After the purification, purified proteins were dissolved in a physiological buffer such as DMEM medium.

TABLE 22  Potentially Best aMTDs (Hydrophobic, Flexible, 240  Bending, Aliphatic & Helical)   Random Peptides 31   No Bending Peptides (No Proline at 5 or 6 and/or 12) 02   No Bending Peptides (No Central Proline) 01   Rigid Peptides (II < 50) 09   Too Much Flexible Peptides 09   Aromatic Peptides (Aromatic Ring Presences) 01   Hydrophobic, But Non-Aromatic Peptides 02   Hydrophilic, But Non-Aliphatic Peptides 07

4-3. Expression of aMTD- or Random Peptide (rP)-Fused Recombinant Proteins

Using the standardized six critical factors, 316 aMTD sequences have been designed. In addition, 141 rPeptides are also developed that lack one of these critical factors: no bending peptides: i) absence of proline both in the middle and at the end of sequence or ii) absence of proline either in the middle or at the end of sequence, rigid peptides, too much flexible peptides, aromatic peptides (aromatic ring presence), hydrophobic but non-aromatic peptides, and hydrophilic but non-aliphatic peptides (Table 22).

These rPeptides are devised to be compared and contrasted with aMTDs in order to analyze structure/sequence activity relationship (SAR) of each critical factor with regard to the peptides' intracellular delivery potential. All peptide (aMTD or rPeptide)-containing recombinant proteins have been fused to the CRA to enhance the solubility of the recombinant proteins to be expressed, purified, prepared and analyzed.

These designed 316 aMTDs and 141 rPeptides fused to CRA were all cloned (FIG. 2) and tested for inducible expression in E. coli (FIG. 3). Out of these peptides, 240 aMTDs were inducibly expressed, purified and prepared in soluble form (FIG. 4). In addition, 31 rPeptides were also prepared as soluble form (FIG. 4).

To prepare the proteins fused to rPeptides, 60 proteins were expressed that were 10 out of 26 rPeptides in the category of no bending peptides (Table 16); 15 out of 23 in the category of rigid peptides [instability index (II)<40] (Table 17); 19 out of 24 in the category of too much flexible peptides (Table 18); 6 out of 27 in the category of aromatic peptides (Table 19); 8 out of 23 in the category of hydrophobic but non-aromatic peptides (Table 20); and 12 out of 18 in the category of hydrophilic but non-aliphatic peptides (Table 21).

4-4. Quantitative Cell-Permeability of aMTD-Fused Recombinant Proteins

The aMTDs and rPeptides were fluorescently labeled and compared based on the critical factors for cell-permeability by using flow cytometry and confocal laser scanning microscopy (FIGS. 5 to 8). The cellular uptake of the peptide-fused non-functional cargo recombinant proteins could quantitatively be evaluated in flow cytometry, while confocal laser scanning microscopy allows intracellular uptake to be assessed visually. The analysis included recombinant proteins fused to a negative control [rP38] that has opposite characteristics (hydrophilic and aromatic sequence: YYNQSTCGGQCY) to the aMTDs (hydrophobic and aliphatic sequences). Relative cell-permeability (relative fold) of aMTDs to the negative control was also analyzed (Table 23 and FIG. 9).

Table 23 shows Comparison Analysis of Cell-Permeability of aMTDs with a Negative Control (A: rP38).

TABLE 23 Negative Control rP38 aMTD 19.6 ± 1.6* The Average of 240 aMTDs (Best: 164.2) *Relative Fold (aMTD in Geo Mean in its comparison to rP38)

Relative cell-permeability (relative fold) of aMTDs to the reference CPPs [B: MTM12 (AAVLLPVLLAAP)(SEQ ID NO: 940), C: MTD85 (AVALLILAV)(SEQ ID NO: 941)] was also analyzed (Tables 40 and 41)

Table 24 shows Comparison Analysis of Cell-Permeability of aMTDs with a Reference CPP (B: MTM12).

TABLE 24 MTM12 aMTD 13.1 ± 1.1* The Average of 240 aMTDs (Best: 109.9) *Relative Fold (aMTD in Geo Mean in its comparison to MTM12)

Table 25 shows Comparison Analysis of Cell-Permeability of aMTDs with a Reference CPP (C: MTD85).

TABLE 25 MTD85 aMTD 6.6 ± 0.5* The Average of 240 aMTDs (Best: 55.5) *Relative Fold (aMTD in Geo Mean in its comparison to MTD85)

Geometric means of negative control (histidine-tagged rP38-fused CRA recombinant protein) subtracted by that of naked protein (histidine-tagged CRA protein) lacking any peptide (rP38 or aMTD) was standardized as relative fold of 1. Relative cell-permeability of 240 aMTDs to the negative control (A type) was significantly increased by up to 164 fold, with average increase of 19.6±1.6 (Table 26-31).

TABLE 26 Proline Rigidity/ Sturctural Hydro- Sequence Position Flexibility Feature pathy Relative Ratio (Fold) ID Number aMTD Sequences Length (PP) (II) (AI) (GRAVY) A B C 229 899 AVVIALPAVVAP 12 7 57.3 195.0 2.4 164.2 109.9 55.5 237 908 VALALAPVVVAP 12 7 57.3 195.0 2.3 150.6 100.8 50.9 238 910 VAALLPAVVVAP 12 6 57.3 195.0 2.3 158.5 99.4 50.2 185 810 VIVLAAPALAAP 12 7 50.2 187.5 2.2 120.0 80.3 40.6 233 904 AVLAVVAPVVAP 12 8 57.3 186.7 2.4 105.7 70.8 35.8 74 321 IVAVALPALAVP 12 7 50.2 203.3 2.3 97.8 65.2 32.9 201 851 VLAVVLPAVALP 12 7 57.3 219.2 2.5 96.6 64.7 32.7 239 911 VALALPAVVVAP 12 6 57.3 195.0 2.3 84.8 56.8 28.7 205 852 VLAVAAPAVLLP 12 7 57.3 203.3 2.3 84.6 56.6 28.6 179 803 AIALAVPVLALP 12 7 57.3 211.7 2.4 74.7 50.0 25.3 222 888 ILAVVAIPAAAP 12 8 54.9 187.5 2.3 71.0 47.5 24.0 188 825 IVAVIVAPAVAP 12 8 43.2 195.0 2.5 69.7 46.6 23.6 226 895 AIIIVVPAIAAP 12 7 50.2 211.7 2.5 60.8 40.7 20.6 227 896 AILIVVAPIAAP 12 8 50.2 211.7 2.5 57.5 38.5 19.4 164 727 VALAIALPAVLP 12 8 57.3 211.6 2.3 54.7 36.7 18.5 139 603 VLVALAAPVIAP 12 8 57.3 203.3 2.4 54.1 36.1 18.2 200 847 LVAIVVLPAVAP 12 8 50.2 213.2 2.6 50.2 33.4 16.9 189 826 LVALAAPIIAVP 12 7 41.3 211.7 2.4 49.2 32.9 16.6 161 724 VAVLAVLPALAP 12 8 57.3 203.3 2.3 47.5 31.8 16.1 131 563 ALAVIVVPALAP 12 8 50.2 203.3 2.4 47.1 31.4 15.9 186 811 AAALAVPALAVP 12 7 57.3 195.0 2.3 46.5 31.1 15.7 194 831 IIVAVAPAAIVP 12 7 43.2 203.3 2.5 46.3 31.0 15.7 192 829 AALALVAPVIVP 12 8 50.2 203.3 2.4 44.8 30.0 15.2 224 891 ILAVAAIPAALP 12 8 54.9 195.8 2.2 44.7 29.9 15.1 234 905 AVIAVAPLVVAP 12 7 41.3 195.0 2.4 44.0 29.5 14.9 132 664 VAIALIVPALAP 12 8 50.2 211.7 2.4 43.6 29.1 14.7 34 124 IAVALPALIAAP 12 6 50.3 195.8 2.2 43.6 29.0 14.7 190 827 IAAVLAAPALVP 12 8 57.3 187.5 2.2 43.0 28.8 14.6 2 2 AAAVPLLAVVVP 12 5 41.3 195.0 2.4 40.9 27.2 13.8 91 385 IVAIAVPALVAP 12 7 50.2 203.3 2.4 38.8 25.9 13.1 191 828 IALLAAPIIAVP 12 7 41.3 220.0 2.4 36.8 24.6 12.4 181 806 LVALAVPAAVLP 12 7 57.3 203.3 2.3 36.7 24.6 12.4 198 845 AAVVIAPLLAVP 12 7 41.3 203.3 2.4 35.8 24.0 12.1 218 882 AIALVVPAVAVP 12 7 57.3 195.0 2.4 35.0 23.4 11.8 128 545 VVLVLAAPAAVP 12 8 57.3 195.0 2.3 34.6 23.1 11.7 39 161 AVIALPALIAAP 12 6 57.3 195.3 2.2 34.5 23.0 11.6 110 481 AIAIAIVPVALP 12 8 50.2 211.6 2.4 34.3 23.0 11.6 230 900 ALVAVIAPVVAP 12 8 57.3 195.0 2.4 34.3 22.9 11.6 53 223 AILAVPIAVVAP 12 6 57.3 203.3 2.4 33.0 22.1 11.2 187 824 LIIVAAAPAVAP 12 8 50.2 187.5 2.3 32.8 21.9 11.1 130 562 ALIAAIVPALVP 12 8 50.2 211.7 2.4 32.7 21.8 11.0 52 222 ALLIAPAAVIAP 12 6 57.3 195.8 2.2 32.6 21.7 11.0 17 61 VAALPVLLAALP 12 5 57.3 211.7 2.3 31.2 20.8 10.5 134 583 VAVALIVPALAP 12 8 50.2 203.3 2.4 30.6 20.4 10.3 223 889 ILVAAAPIAALP 12 7 57.3 195.8 2.2 30.3 20.3 10.3 177 787 AVALVPVIVAAP 12 6 50.2 195.0 2.4 29.3 19.6 9.9 157 703 IVAVALVPALAP 12 8 50.2 203.3 2.4 29.2 19.5 9.9 158 705 IVAVALLPALAP 12 8 50.2 211.7 2.4 28.6 19.1 9.7 220 885 LVAIAPAVAVLP 12 6 57.3 203.3 2.4 28.3 19.0 9.6 3 3 AALLVPAAVLAP 12 6 57.3 187.5 2.1 27.0 18.0 9.1 137 601 AAILIAVPIAAP 12 8 57.3 195.8 2.3 26.8 17.9 9.0 196 843 AVLVLVAPAAAP 12 8 41.3 219.2 2.5 26.4 17.7 8.9 94 403 AAALVIPAAILP 12 7 54.9 195.8 2.2 25.2 16.8 8.5 127 544 IVALIVAPAAVP 12 8 43.1 203.3 2.4 23.4 15.6 7.9 121 522 ALLVIAVPAVAP 12 8 57.3 203.3 2.4 22.7 15.2 7.7

TABLE 27 Proline Rigidity/ Sturctural Hydro- Sequence Position Flexibility Feature pathy Relative Ratio (Fold) ID Number aMTD Sequences Length (PP) (II) (AI) (GRAVY) A B C 180 805 LVLIAAAPIALP 12 8 41.3 220.0 2.4 22.3 14.9 7.6 108 464 AVVILVPLAAAP 12 7 57.3 203.3 2.4 22.3 14.9 7.5 96 400 LAAAVIPVAILP 12 7 54.3 211.7 2.4 22.2 14.8 7.5 168 747 VALLAIAPALAP 12 8 57.3 195.8 2.2 22.0 14.8 7.5 115 501 VIVALAVPALAP 12 8 50.2 202.3 2.4 21.5 14.4 7.3 147 661 AAILAPIVAALP 12 6 50.2 195.8 2.2 21.4 14.3 7.2 176 786 LVAIAPLAVLAP 12 6 41.3 211.7 2.4 21.2 14.2 7.2 144 625 ILAAAAAPLIVP 12 8 50.2 195.8 2.2 20.5 13.9 7.0 101 442 ALAALVPAVLVP 12 7 57.3 203.3 2.3 20.4 13.6 6.9 240 912 VALLAPAVVVAP 12 6 57.3 195.0 2.3 19.9 13.3 6.7 43 165 ALAVPVALAIVP 12 5 50.2 203.3 2.4 19.8 13.2 6.7 98 422 VVAILAPLLAAP 12 7 57.3 211.7 2.4 19.6 13.1 6.6 155 595 AALVAVLPVALP 12 8 57.3 203.3 2.3 19.5 13.1 6.6 81 343 IVAVALPALVAP 12 7 50.2 203.3 2.3 19.4 12.9 6.5 76 323 IVAVALPVALAP 12 7 50.2 203.3 2.3 19.1 12.8 6.4 105 461 IAAVIVPAVALP 12 7 50.2 203.3 2.4 19.0 12.7 6.4 9 21 AVALLPALLAVP 12 6 57.3 211.7 2.3 18.9 12.6 6.4 95 404 LAAAVIPAAILP 12 7 54.3 195.8 2.2 18.5 12.6 6.4 60 261 LVLVPLLAAAAP 12 5 41.3 211.6 2.3 18.5 12.3 6.2 122 524 AVALIVVPALAP 12 8 50.2 203.3 2.4 18.3 12.2 6.2 55 225 VAALLPAAAVLP 12 6 57.3 187.5 2.1 18.3 12.2 6.1 63 264 LAAAPVVIVIAP 12 5 50.2 203.3 2.4 18.2 12.1 6.0 1 1 AAALAPVVLALP 12 6 57.3 187.5 2.1 17.7 11.8 6.0 88 283 AAALVIPAIALP 12 7 54.3 195.8 2.2 17.7 11.8 5.9 107 463 AVAILVPLLAAP 12 7 57.3 211.7 2.4 17.6 11.7 5.9 75 322 VVAIVLPALAAP 12 7 50.2 203.3 2.3 17.6 11.7 5.9 117 503 AAIIIVLPAALP 12 8 50.2 220.0 2.4 17.6 11.6 5.6 211 870 VLVAAVLPIAAP 12 8 41.3 203.3 2.4 16.6 11.1 5.6 56 241 AAAVVPVLLVAP 12 8 57.3 195.0 2.4 16.6 11.0 5.6 163 726 LAVAIIAPAVAP 12 8 57.3 187.5 2.2 16.5 11.0 5.5 79 341 IVAVALPAVLAP 12 7 50.2 203.3 2.3 16.4 10.9 5.5 123 542 ALALIIVPAVAP 12 8 50.2 211.6 2.4 16.2 10.8 5.4 83 361 AVVIVAPAVIAP 12 7 50.2 195.0 2.4 16.0 10.7 5.3 54 224 ILAAVPIALAAP 12 8 57.2 195.8 2.2 15.8 10.6 5.3 111 482 ILAVAAIPVAVP 12 8 54.3 203.3 2.4 15.8 10.6 5.3 20 54 AIVALPVAVLAP 12 6 50.2 203.3 2.4 15.8 10.6 5.3 113 484 LAVVLAAPAIVP 12 8 50.2 203.3 2.4 15.6 10.4 5.0 210 868 VLVAAILPAAIP 12 8 54.3 211.7 2.4 14.9 10.0 5.0 124 541 LLALIIAPAAAP 12 8 57.3 204.1 2.1 14.8 9.9 5.0 150 666 AAIAIIAPAIVP 12 8 50.2 195.8 2.0 14.7 9.9 5.0 147 665 LAIVLAAPVAVP 12 8 50.2 203.3 2.3 14.7 9.9 4.9 84 363 AVLAVAPALIVP 12 7 50.2 203.3 2.3 14.7 9.8 4.9 57 242 AALLVPALVAAP 12 6 57.3 187.5 2.1 14.6 9.7 4.7 90 384 VIVAIAPALLAP 12 7 50.2 211.6 2.4 14.0 9.4 4.7 214 877 VAIIAVPAVVAP 12 7 57.3 195.0 2.4 14.0 9.4 4.7 206 863 AAVVLLPIIAAP 12 7 41.3 211.7 2.4 13.8 9.3 4.7 123 525 ALAIVVAPVAVP 12 8 50.2 195.0 2.4 13.8 9.2 4.7 213 875 AIAIVVPAVAVP 12 7 50.2 195.0 2.4 13.8 9.2 4.7 69 285 AIVLLPAAVVAP 12 6 50.2 203.3 2.4 13.3 8.9 4.5 65 281 ALIVLPAAVAVP 12 6 50.2 203.3 2.4 13.3 8.9 4.6 209 867 ALLVVIAPLAAP 12 8 41.3 211.7 2.4 13.2 8.8 4.4 172 766 IVVIAVAPAVAP 12 8 50.2 195.0 2.4 12.9 8.6 4.4 80 342 VIVALAPAVLAP 12 7 50.2 203.3 2.3 12.7 8.5 4.3 217 881 AALIVVPAVAVP 12 7 50.2 195.0 2.4 12.7 8.5 4.3 119 506 AIIIVIAPAAAP 12 8 50.2 195.2 2.3 12.4 8.3 4.2

TABLE 28 Proline Rigidity/ Sturctural Hydro- Sequence Position Flexibility Feature pathy Relative Ratio (Fold) ID Number aMTD Sequences Length (PP) (II) (AI) (GRAVY) A B C 169 763 VAVLIAVPALAP 12 8 57.3 203.3 2.3 12.0 7.2 4.2 159 706 IVAVALLPAVAP 12 8 50.2 203.3 2.4 12.0 7.0 4.1 156 687 AILAVALPLLAP 12 8 57.3 220.3 2.3 12.0 7.0 4.1 145 643 LALVLAAPAIVP 12 8 50.2 211.6 2.4 11.8 7.9 4.0 66 282 VLAVAPALIVAP 12 6 50.2 203.3 2.4 11.8 7.9 4.0 126 543 LLAALIAPAALP 12 8 57.3 204.1 2.1 11.7 7.8 4.0 78 325 IVAVALPAVALP 12 7 50.2 203.3 2.3 11.7 7.8 4.0 199 846 IAVAVAAPLLVP 12 8 41.3 203.3 2.4 11.7 6.8 4.0 89 383 VIVALAPALLAP 12 7 50.2 211.6 2.3 11.6 7.7 3.9 87 381 VVAIVLPAVAAP 12 7 50.2 195.0 2.4 11.5 7.7 3.9 183 808 LVVLAAAPLAVP 12 8 41.3 203.3 2.3 11.5 7.6 3.9 208 865 AVLVIAVPAIAP 12 8 57.3 203.3 2.5 11.3 7.5 3.8 162 725 IAVLAVAPAVLP 12 8 57.3 203.3 2.3 11.2 7.5 3.8 197 844 VVALLAPLIAAP 12 7 41.3 211.8 2.4 11.2 7.5 3.8 228 897 AVIVPVAIIAAP 12 5 50.2 203.3 2.5 11.2 7.5 3.8 141 605 VIAAVLAPVAVP 12 8 57.3 195.0 2.4 11.0 7.4 3.7 166 744 AAVVIVAPVALP 12 8 50.2 195.0 2.4 11.0 7.3 3.7 51 221 AAILAPIVALAP 12 6 50.2 195.8 2.2 10.9 7.3 3.7 142 622 ALIVLAAPVAVP 12 8 50.2 203.3 2.4 10.6 7.1 3.6 92 401 AALAVIPAAILP 12 7 54.9 195.8 2.2 10.6 7.1 3.6 77 324 IVAVALPAALVP 12 7 50.2 203.3 2.3 10.3 6.9 3.5 215 878 IVALVAPAAVVP 12 7 50.2 195.0 2.4 10.3 6.9 3.5 71 302 LALAPALALLAP 12 5 57.3 204.2 2.1 10.2 6.8 3.4 154 685 ALLVAVLPAALP 12 8 57.3 211.7 2.3 10.2 5.9 3.4 201 848 AVAIVVLPAVAP 12 8 50.2 195.0 2.4 10.0 6.7 3.4 138 602 VIVALAAPVLAP 12 8 50.2 203.3 2.4 9.9 5.8 3.4 178 788 AIAVAIAPVALP 12 8 57.3 187.5 2.3 9.8 6.6 3.3 38 145 LLAVVPAVALAP 12 6 57.3 203.3 2.3 9.5 6.3 3.2 6 11 VVALAPALAALP 12 6 57.3 187.5 2.1 9.5 6.3 3.2 35 141 AVIVLPALAVAP 12 6 50.2 203.3 2.4 9.4 6.3 3.2 120 521 LAALIVVPAVAP 12 8 50.2 203.3 2.4 9.4 6.3 3.2 100 425 AVVAIAPVLALP 12 7 57.3 203.3 2.4 9.4 6.3 3.2 86 365 AVIVVAPALLAP 12 7 50.2 203.3 2.3 9.3 6.2 3.1 62 263 ALAVIPAAAILP 12 6 54.9 195.8 2.2 9.0 6.0 3.0 82 345 ALLIVAPVAVAP 12 7 50.2 203.3 2.3 8.9 5.9 3.0 203 850 LVIALAAPVALP 12 8 57.3 211.7 2.4 8.8 5.9 3.0 37 144 VLAIVPAVALAP 12 6 50.2 203.3 2.4 8.8 5.9 3.0 173 767 IVVAAVVPALAP 12 8 50.2 195.0 2.4 8.5 5.0 2.9 47 185 AALVLPLIIAAP 12 6 41.3 220.0 2.4 8.5 5.7 2.9 202 849 AVILLAPLIAAP 12 7 57.3 220.0 2.4 8.3 4.8 2.8 207 864 ALLVIAPAIAVP 12 7 57.3 211.7 2.4 8.2 4.8 2.8 40 162 AVVALPAALIVP 12 6 50.2 203.3 2.4 8.2 5.5 2.8 42 164 LAAVLPALLAAP 12 6 57.3 195.8 2.1 8.2 5.5 2.8 234 907 VAIALAPVVVAP 12 7 57.3 195.0 2.4 8.1 5.4 2.8 103 444 LAAALVPVALVP 12 7 57.3 203.3 2.3 8.1 5.4 2.7 102 443 ALAALVPVALVP 12 7 57.3 203.3 2.3 8.0 5.3 2.7 231 901 ALVAVLPAVAVP 12 7 57.3 195.0 2.4 7.7 5.1 2.6 221 887 VLAVAPAVAVLP 12 6 57.3 195.0 2.4 7.7 5.1 2.6 167 746 VAIIVVAPALAP 12 8 50.2 203.3 2.4 7.6 4.4 2.6 232 902 ALVAPLLAVAVP 12 5 41.3 203.3 2.3 7.6 5.1 2.6 133 565 VAIVLYAPAVAP 12 8 50.2 195.0 2.4 7.5 5.0 2.5 59 245 AAALAPVLALVP 12 6 57.3 187.5 2.1 7.5 5.0 2.5 165 743 AIAIALVPVALP 12 8 57.3 211.6 2.4 7.4 4.9 2.5 109 465 AVVILVPLAAAP 12 7 57.3 203.3 2.4 7.4 4.9 2.5 30 104 AVVAAPLVLALP 12 6 41.3 203.3 2.3 7.3 4.9 2.5

TABLE 29 Proline Rigidity/ Sturctural Hydro- Sequence Position Flexibility Feature pathy Relative Ratio (Fold) ID Number aMTD Sequences Length (PP) (II) (AI) (GRAVY) A B C 160 707 IVALAVLPAVAP 12 8 50.2 203.3 2.4 7.3 4.9 2.5 212 872 VLAAAVLPLVVP 12 8 41.3 219.2 2.5 7.3 4.9 2.5 135 883 AVILALAPIVAP 12 8 50.2 211.6 2.4 7.3 4.8 2.4 216 879 AAIVLLPAVVVP 12 7 50.2 219.1 2.5 7.2 4.8 2.4 175 784 VAALPAVALVVP 12 5 57.3 195.0 2.4 7.1 4.7 2.4 225 890 VIAIPAILAAAP 12 5 54.9 195.8 2.3 7.0 4.7 2.4 8 13 AAALVPVVALLP 12 6 57.3 203.3 2.3 7.0 4.7 2.4 184 809 LIVLAAPALAAP 12 7 50.2 195.8 2.2 7.0 4.7 2.4 104 445 ALAALVPALVVP 12 7 57.3 203.3 2.3 6.9 4.6 2.3 22 81 AALLPALAALLP 12 5 57.3 204.2 2.1 6.9 4.6 2.3 151 667 LAVAIVAPALVP 12 8 50.2 203.3 2.3 6.9 4.6 2.3 235 906 AVIALAPVVVAP 12 7 57.3 195.0 2.4 6.8 4.6 2.3 112 483 ILAAAIIPAALP 12 8 54.9 204.1 2.2 6.8 4.5 2.3 114 485 AILAAIVPLAVP 12 8 50.2 211.6 2.4 6.8 4.5 2.3 97 421 AAILAAPLIAVP 12 7 57.3 195.8 2.2 6.7 4.5 2.3 136 585 ALIVAIAPALVP 12 8 50.2 211.6 2.4 6.6 4.4 2.2 99 424 AVVVAAPVLALP 12 7 57.3 195.0 2.4 6.6 4.4 2.2 85 364 LVAAVAPALIVP 12 7 50.2 203.3 2.3 6.5 4.3 2.2 93 402 ALAAVIPAAILP 12 7 54.9 195.8 2.2 6.4 4.3 2.2 106 462 IAAVLVPAVALP 12 7 57.3 203.3 2.4 6.3 4.2 2.1 64 265 VLAIAPLLAAVP 12 6 41.3 211.6 2.3 6.0 4.0 2.0 70 301 VIAAPVLAVLAP 12 6 57.3 203.3 2.4 6.0 4.0 2.0 45 180 LLAAPVVIALAP 12 6 57.3 211.6 2.4 6.0 4.0 2.0 58 243 AAVLLPVALAAP 12 6 57.3 187.5 2.1 5.9 3.9 2.0 148 664 ILIAIAIPAAAP 12 8 54.9 204.1 2.3 5.7 3.8 1.9 174 780 IVALVPAVAIAP 12 6 50.2 203.3 2.5 5.7 3.8 1.9 116 502 AIVALAVPVLAP 12 8 50.2 203.3 2.4 5.6 3.7 1.9 61 262 ALIAVPAIIVAP 12 6 50.2 211.6 2.4 5.5 3.7 1.9 152 680 LAIVLAAPAVLP 12 8 50.2 211.7 2.4 5.5 3.2 1.9 193 830 IALVAAPVALVP 12 7 57.3 203.3 2.4 5.3 3.5 1.8 170 764 AVALAVLPAVVP 12 8 57.3 195.0 2.3 5.0 3.4 1.7 182 807 AVALAVPALVLP 12 7 57.3 203.3 2.3 5.5 3.3 1.7 46 184 LAAIVPAIIAVP 12 6 50.2 211.6 2.4 4.8 3.2 1.6 73 305 IALAAPILLAAP 12 6 57.3 204.2 2.2 4.8 3.2 1.6 27 101 LVALAPVAAVLP 12 6 57.3 203.3 2.3 4.5 3.0 1.5 72 304 AIILAPIAAIAP 12 6 57.3 204.2 2.3 4.4 3.0 1.5 140 604 VALIAVAPAVVP 12 8 57.3 195.0 2.4 4.3 2.5 1.5 146 645 ALAVVALPAIVP 12 8 50.2 203.3 2.4 4.3 2.9 1.5 48 201 LALAVPALAALP 12 6 57.3 195.8 2.1 4.2 2.8 1.4 41 163 LALVLPAALAAP 12 6 57.3 195.8 2.1 4.1 2.4 1.4 195 832 AVAAIVPVIVAP 12 7 40.2 195.0 2.5 4.1 2.7 1.4 44 182 ALIAPVVALVAP 12 6 57.3 203.3 2.4 4.0 2.7 1.4 11 20 VVLVLPAAAAVP 12 6 57.3 195.0 2.4 4.0 2.6 1.3 31 105 LLALAPAALLAP 12 6 57.3 204.1 2.1 4.0 2.6 1.3 129 561 AAVAIVLPAVVP 12 8 50.2 195.0 2.4 3.9 2.6 1.3 171 765 AVALAVVPAVLP 12 8 57.3 195.0 2.3 3.8 2.2 1.3 153 684 AAIVLALPAVLP 12 8 50.2 211.7 2.4 3.5 2.1 1.2 36 143 AVLAVPAVLVAP 12 6 57.3 195.0 2.4 3.3 2.2 1.1 118 504 LIVALAVPALAP 12 8 50.2 211.7 2.4 3.3 2.2 1.1 10 22 AVVLVPVLAAAP 12 6 57.3 195.0 2.4 3.1 2.1 1.1 5 5 AAALLPVALVAP 12 6 57.3 187.5 2.1 3.1 2.1 1.0 67 283 AALLAPALIVAP 12 6 50.2 195.8 2.2 3.1 2.0 1.0 21 65 IAIVAPVVALAP 12 6 50.2 203.3 2.4 3.0 2.0 1.0 219 883 LAIVPAAIAALP 12 6 50.2 195.8 2.2 3.0 2.0 1.0 33 123 AAIIVPAALLAP 12 6 50.2 195.8 2.2 2.9 2.0 1.0

TABLE 30 Sequence Proline Rigidity/ Sturctural Hydro- ID Position Flexibility Feature pathy Relative Ratio (Fold) Number aMTD Sequences Length (PP) (II) (AI) (GRAVY) A B C 68  284 ALIAPAVALIVP 12 5 50.2 211.7 2.4 2.8 1.8 0.9 50 205 ALALVPAIAALP 12 6 57.3 195.8 2.2 2.6 1.7 0.9 14 42 VAALPVVAVVAP 12 5 57.3 186.7 2.4 2.5 1.7 0.8 32 121 AIVALPALALAP 12 6 50.2 195.8 2.2 2.5 1.7 0.8 13 25 IVAVAPALVALP 12 6 50.2 203.3 2.4 2.4 1.6 0.8 12 24 IALAAPALIVAP 12 6 50.2 195.8 2.2 2.3 1.6 0.8 49 204 LIAALPAVAALP 12 6 57.3 195.8 2.2 2.2 1.5 0.8 7 12 LLAAVPAVLLAP 12 6 57.3 211.7 2.3 2.2 1.5 0.7 15 43 LLAAPLVVAAVP 12 5 41.3 187.5 2.1 2.1 1.4 0.7 29 103 ALIAAPILALAP 12 6 57.3 204.2 2.2 2.1 1.4 0.7 23 82 AVVLAPVAAVLP 12 6 57.3 195.0 2.4 2.1 1.4 0.7 4 4 ALALLPVAALAP 12 6 57.3 195.8 2.1 2.0 1.3 0.7 26 85 LLVLPAAALAAP 12 5 57.3 195.8 2.1 1.9 1.3 0.7 19 60 AALLVPALVAVP 12 6 57.3 203.3 2.3 1.9 1.3 0.7 16 44 ALAVPVALLVAP 12 5 57.3 203.3 2.3 1.8 1.1 0.5 25 84 AAVAAPLLLALP 12 6 41.3 195.8 2.1 1.5 1.0 0.5 18 62 VALLAPVALAVP 12 6 57.3 203.3 2.3 1.4 0.9 0.5 24 83 LAVAAPLALALP 12 6 41.3 195.8 2.1 1.4 0.9 0.5 28 102 LALAPAALALLP 12 5 57.3 204.2 2.1 1.4 0.9 0.5 143 620 VAAAIALPAIVP 12 8 50.2 187.5 2.3 0.8 0.6 0.3 19.6 ± 1.6 13.1 ± 1.1 8.6 ± 0.5

Moreover, compared to reference CPPs (B type: MTM12 and C type: MTD85), novel 240 aMTDs averaged of 13±1.1 (maximum 109.9) and 6.6±0.5 (maximum 55.5) fold higher cell-permeability, respectively (Tables 26-31).

TABLE 31 Negative control rP38 MTM12 MTD85 aMTD 19.6 ± 1.6* 13.1 ± 1.1* 6.6 ± 0.5* The Average of (Best: 164.2) (Best: 109.9) (Best: 55.5) 240 aMTDs *Relative Fold (aMTD in Geo Mean in its comparison to rP38, MTM12 or MTD85)

In addition, cell-permeability of 31 rPeptides has been compared with that of 240 aMTDs (0.3±0.04; Tables 32 and 33).

TABLE 32 Proline Rigidity/ Sturctural Hydro- SEQ ID Position Flexibility Feature pathy Relative Ratio NOs ID Sequence Length (PP) (II) (AI) (GRAVY) to aMTD AVE 894 692 PAPLPPVVILAV 12 1, 3, 5, 6 105.5 186.7 1.8 0.74 882 26 AAIALAAPLAIV 12 8 18.1 204.2 2.5 0.65 878 113 PVAVALLIAVPP 12 1, 11, 12 57.3 195.0 2.1 0.61 884 466 IIAAAAPLAIIP 12 7, 12 22.8 204.2 2.3 0.52 885 167 VAIAIPAALAIP 12 6, 12 20.4 195.8 2.3 0.50 923 97 ALLAAPPALLAL 12 6, 7 57.3 204.2 2.1 0.41 896 190 VPLLVPVVPVVP 12 2, 6, 9, 12 105.4 210.0 2.2 0.41 887 426 AAALAIPLAIIP 12 7, 12 4.37 204.2 2.2 0.40 924 214 ALIVAPALMALP 12 6, 12 60.5 187.5 2.2 0.33 900 68 VAPVLPAAPLVP 12 3, 6, 9, 12 105.5 162.5 1.6 0.32 928 39 CYNTSPCTGCCY 12 6 52.5 0.0 0.0 0.29 875 934 LILAPAAVVAAA 12 5 57.3 195.8 2.5 0.28 903 938 VPVLLPVVVPVP 12 2, 6, 10, 12 121.5 210.0 2.2 0.28 904 329 LPVLVPVVPVVP 12 2, 6, 9, 12 121.5 210.0 2.2 0.23 888 606 AAAIAAIPIIIP 12 8, 12 4.4 204.2 2.4 0.20 905 49 VVPAAPAVPVVP 12 3, 6, 9, 12 121.5 145.8 1.7 0.18 931 139 TGSTNSPTCTST 12 7 53.4 0.0 −0.7 0.17 906 772 LPVAPVIPIIVP 12 2, 5, 8, 12 79.9 210.8 2.1 0.16 918 921 IWWFVVLPLVVP 12 8, 12 41.3 194.2 2.2 0.14 889 66 AGVLGGPIMGVP 12 7, 12 35.5 121.7 1.3 0.13 909 693 AAPVLPVAVPIV 12 3, 6, 10 82.3 186.7 2.1 0.13 932 18 NYCCTPTTNGQS 12 6 47.9 0.0 −0.9 0.10 877 16 NNSCTTYTNGSQ 12 None 47.4 0.0 −1.4 0.08 891 227 LAAIVPIAAAVP 12 6, 12 34.2 187.5 2.2 0.08 892 17 GGCSAPQTTCSN 12 6  51.6 8.3 −0.5 0.08 893 67 LDAEVPLADDVP 12 6, 12 34.2 130.0 0.3 0.08 934 635 GSTGGSQQNNQY 12 None 31.9 0.0 −1.9 0.07 911 29 VLPPLPVLPVLP 12 3, 4, 6, 9, 12 121.5 202.5 1.7 0.07 936 57 QNNCNTSSQGGG 12 None 52.4 0.0 −1.6 0.06 938 700 GTSNTCQSNQNS 12 None 19.1 0.0 −1.6 0.05 939 38 YYNQSTCGGQCY 12 ND 53.8 0.0 −1.0 0.05 AVE 0.3 ± 0.04

TABLE 33 Relative Ratio to aMTD AVE* rPeptide 0.3 ± 0.04 The Average of 31 aMTDs *Out of 240 aMTDs, average relative fold of aMTD had been 19.6 fold compared to type A (rP38).

In summary, relative cell-permeability of aMTDs has shown maximum of 164.0, 109.9 and 55.5 fold higher to rP38, MTM12 and MTD85, respectively. In average of total 240 aMTD sequences, 19.6±1.6, 13.1±1.1 and 6.6±0.5 fold higher cell-permeability are shown to the rP38, MTM12 and MTD85, respectively (Tables 26-31). Relative cell-permeability of negative control (rP38) to the 240 aMTDs is only 0.3±0.04 fold.

4-5. Intracellular Delivery and Localization of aMTD-Fused Recombinant Proteins

Recombinant proteins fused to the aMTDs were tested to determine their intracellular delivery and localization by laser scanning confocal microscopy with a negative control (rP38) and previous published CPPs (MTM12 and MTD85) as the positive control references. NIH3T3 cells were exposed to 10 μM of FITC-labeled protein for 1 hour at 37, and nuclei were counterstained with DAPI. Then, cells were examined by confocal laser scanning microscopy (FIG. 7). Recombinant proteins fused to aMTDs clearly display intracellular delivery and cytoplasmic localization (FIG. 7) that are typically higher than the reference CPPs (MTM12 and MTD85). The rP38-fused recombinant protein did not show internalized fluorescence signal (FIG. 7a ). In addition, as seen in FIG. 8, rPeptides (his-tagged CRA recombinant proteins fused to each rPeptide) display lower- or non-cell-permeability.

4-6. Summary of Quantitative and Visual Cell-Permeability of Newly Developed aMTDs

Histidine-tagged aMTD-fused cargo recombinant proteins have been greatly enhanced in their solubility and yield. Thus, FITC-conjugated recombinant proteins have also been tested to quantitate and visualize intracellular localization of the proteins and demonstrated higher cell-permeability compared to the reference CPPs.

In the previous studies using the hydrophobic signal-sequence-derived CPPs—MTS/MTM or MTDs, 17 published sequences have been identified and analyzed in various characteristics such as length, molecular weight, pI value, bending potential, rigidity, flexibility, structural feature, hydropathy, amino acid residue and composition, and secondary structure of the peptides. Based on these analytical data of the sequences, novel artificial and non-natural peptide sequences designated as advanced MTDs (aMTDs) have been invented and determined their functional activity in intracellular delivery potential with aMTD-fused recombinant proteins.

aMTD-fused recombinant proteins have promoted the ability of protein transduction into the cells compared to the recombinant proteins containing rPeptides and/or reference hydrophobic CPPs (MTM12 and MTD85). According to the results, it has been demonstrated that critical factors of cell-penetrating peptide sequences play a major role to determine peptide-mediated intracellular delivery by penetrating plasma membrane. In addition, cell-permeability can considerably be improved by following the rational that all satisfy the critical factors.

5. Structure/Sequence Activity Relationship (SAR) of aMTDs on Delivery Potential

After determining the cell-permeability of novel aMTDs, structure/sequence activity relationship (SAR) has been analyzed for each critical factor in selected some of and all of novel aMTDs (FIGS. 13 to 16 and Table 34).

TABLE 34 Rank of Rigidity/ Sturctural Relative Amino Acid Delivery Flexibility Feature Hydropathy Ratio (Fold) Composition Potential (II) (Al) (GRAVY) A B C A V I L  1~10 55.9 199.2 2.3 112.7 75.5 38.1 4.0 3.5 0.4 2.1 11~20 51.2 205.8 2.4 56.2 37.6 19.0 4.0 2.7 1.7 1.6 21~30 49.1 199.2 2.3 43.6 28.9 14.6 4.3 2.7 1.4 1.6 31~40 52.7 201.0 2.4 34.8 23.3 11.8 4.2 2.7 1.5 1.6 41~50 53.8 201.9 2.3 30.0 20.0 10.1 4.3 2.3 1.1 2.3 51~60 51.5 205.2 2.4 23.5 15.7 7.9 4.4 2.1 1.5 2.0 222~231 52.2 197.2 2.3 2.2 1.5 0.8 4.5 2.1 1.0 2.4 232~241 54.1 199.7 2.2 1.7 1.2 0.6 4.6 1.7 0.2 3.5

5-1. Proline Position:

In regards to the bending potential (proline position: PP), aMTDs with its proline at 7′ or 8′ amino acid in their sequences have much higher cell-permeability compared to the sequences in which their proline position is at 5′ or 6′ (FIGS. 14a, 14b, 15a and 15 b).

5-2. Hydropathy:

In addition, when the aMTDs have GRAVY (Grand Average of Hydropathy) ranging in 2.1-2.2, these sequences display relatively lower cell-permeability, while the aMTDs with 2.3-2.6 GRAVY are shown significantly higher one (FIGS. 14c, 14d, 15c and 15d ).

5-3. rPeptide SAR:

To the SAR of aMTDs, rPeptides have shown similar SAR correlations in the cell-permeability, pertaining to their proline position (PP) and hydropathy (GRAVY). These results confirms that rPeptides with high GRAVY (2.4˜2.6) have better cell-permeability (FIG. 16).

5-4. Analysis of Amino Acid Composition:

In addition to proline position and hydropathy, the difference of amino acid composition is also analyzed. Since aMTDs are designed based on critical factors, each aMTD-fused recombinant protein has equally two proline sequences in the composition. Other hydrophobic and aliphatic amino acids—alanine, isoleucine, leucine and valine—are combined to form the rest of aMTD peptide sequences.

Alanine: In the composition of amino acids, the result does not show a significant difference by the number of alanine in terms of the aMTD's delivery potential because all of the aMTDs have three to five alanines. In the sequences, however, four alanine compositions show the most effective delivery potential (geometric mean) (FIG. 13a and FIG. 13b ).

Leucine and Isoleucine: Also, the compositions of isoleucine and leucine in the aMTD sequences show inverse relationship between the number of amino acid (I and L) and delivery potential of aMTDs. Lower number of isoleucine and leucine in the sequences tends to have higher delivery potential (geometric mean) (FIGS. 13a through 13d )

Valine: Conversely, the composition of valine of aMTD sequences shows positive correlation with their cell-permeability. When the number of valine in the sequence is low, the delivery potential of aMTD is also relatively low (FIG. 13c and FIG. 13d )

Ten aMTDs having the highest cell-permeability are selected (average geometric mean: 2584±126). Their average number of valine in the sequences is 3.5; 10 aMTDs having relatively low cell-permeability (average geometric mean: 80±4) had average of 1.9 valine amino acids. The average number of valine in the sequences is lowered as their cell-permeability is also lowered as shown in FIG. 13c and FIG. 13d . Compared to higher cell-permeable aMTDs group, lower sequences had average of 1.9 in their valine composition. Therefore, to obtain high cell-permeable sequence, an average of 2-4 valines should be composed in the sequence.

5-5. Conclusion of SAR Analysis:

As seen in FIG. 15, all 240 aMTDs have been examined for these association of the cell-permeability and the critical factors: bending potential (PP), rigidity/flexibility (II), structure feature (AI), and hydropathy (GRAVY), amino acid length and composition. Through this analysis, cell-permeability of aMTDs tends to be lower when their central proline position is at 5′ or 6′ and GRAVY is 2.1 or lower (FIG. 15). Moreover, after investigating 10 higher and 10 lower cell-permeable aMTDs, these trends are clearly shown to confirm the association of cell-permeability with the central proline position and hydropathy.

6. Experimental Confirmation of Index Range/Feature of Critical Factors

The range and feature of five out of six critical factors have been empirically and experimentally determined that are also included in the index range and feature of the critical factors initially proposed before conducting the experiments and SAR analysis. In terms of index range and feature of critical factors of newly developed 240 aMTDs, the bending potential (proline position: PP), rigidity/flexibility (Instability Index: II), structural feature (Aliphatic Index: AI), hydropathy (GRAVY), amino acid length and composition are all within the characteristics of the critical factors derived from analysis of reference hydrophobic CPPs.

Therefore, our hypothesis to design and develop new hydrophobic CPP sequences as advanced MTDs is empirically and experimentally proved and demonstrated that critical factor-based new aMTD rational design is correct.

TABLE 35 Summarized Critical Factors of aMTD Analysis of Newly Designed Experimental CPPs Results Critical Factor Range Range Bending Potential Proline presences Proline presences (Proline Position: PP) in the middle in the middle (5′, 6′, 7′ (5′, 6′, 7′ or 8′) and at the or 8′) and at the end of peptides end of peptides Rigidity/Flexibility 40-60 41.3-57.3 (Instability Index: II) Structural Feature 180-220 187.5-220.0 (Aliphatic Index: AI) Hydropathy 2.1-2.6 2.2-2.6 (Grand Average of Hydropathy GRAVY) Length  9-13 12 (Number of Amino Acid) Amino acid Composition A, V, I, L, P A, V, I, L, P 7. Discovery and Development of Protein-Based New Biotherapeutics with MITT Enabled by aMTDs for Protein Therapy

Total of 240 aMTD sequences have been designed and developed based on the critical factors. Quantitative and visual cell-permeability of 240 aMTDs (hydrophobic, flexible, bending, aliphatic and 12 a/a-length peptides) are all practically determined.

To measure the cell-permeability of aMTDs, rPeptides have also been designed and tested. As seen in FIGS. 13 to 15, there are vivid association of cell-permeability and the critical factors of the peptides. Out of these critical factors, we are able to configure that the most effective cell-permeable aMTDs have the amino acid length of 12; composition of A, V, L, I and P; multiple proline located at either 7′ or 8′ and at the end (12′); instability index ranged of 41.3-57.3; aliphatic index ranged of 187.5-220.0; and hydropathy (GRAVY) ranged of 2.2-2.6.

These examined critical factors are within the range that we have set for our critical factors; therefore, we are able to confirm that the aMTDs that satisfy these critical factors have relatively high cell-permeability and much higher intracellular delivery potential compared to reference hydrophobic CPPs reported during the past two decades.

It has been widely evident that many human diseases are caused by proteins with deficiency or over-expression that causes mutations such as gain-of-function or loss-of-function. If biologically active proteins could be delivered for replacing abnormal proteins within a short time frame, possibly within an hour or two, in a quantitative manner, the dosage may be regulated depending on when and how proteins may be needed. By significantly improving the solubility and yield of novel aMTD in this invention (Table 31), one could expect its practical potential as an agent to effectively deliver therapeutic macromolecules such as proteins, peptides, nucleic acids, and other chemical compounds into live cells as well as live mammals including human. Therefore, newly developed MITT utilizing the pool (240) of novel aMTDs can be used as a platform technology for discovery and development of protein-based biotherapeutics to apprehend intracellular protein therapy after determining the optimal cargo-aMTD relationship.

The following examples are presented to aid practitioners of the invention, to provide experimental support for the invention, and to provide model protocols. In no way are these examples to be understood to limit the invention.

Example 1. Development of Novel Advanced Macromolecule Transduction Domain (aMTD)

H-regions of signal sequences (HRSP)-derived CPPs (MTS/MTM and MTD) do not have a common sequence, a sequence motif, and/or a common structural homologous feature. In this invention, the aim is to develop improved hydrophobic CPPs formatted in the common sequence and structural motif that satisfy newly determined ‘critical factors’ to have a ‘common function,’ to facilitate protein translocation across the plasma membrane with similar mechanism to the analyzed CPPs.

The structural motif as follows:

In Table 9, universal common sequence/structural motif is provided as follows. The amino acid length of the peptides in this invention ranges from 9 to 13 amino acids, mostly 12 amino acids, and their bending potentials are dependent with the presence and location of proline in the middle of sequence (at 5′, 6′, 7′ or 8′ amino acid) and at the end of peptide (at 12′) for recombinant protein bending. Instability index (II) for rigidity/flexibility of aMTDs is II<40, grand average of hydropathy (GRAVY) for hydropathy is around 2.2, and aliphatic index (AI) for structural features is around 200 (Table 9). Based on these standardized critical factors, new hydrophobic peptide sequences, namely advanced macromolecule transduction domain peptides (aMTDs), in this invention have been developed and summarized in Tables 10 to 15.

Example 2. Construction of Expression Vectors for Recombinant Proteins Fused to aMTDs

Our newly developed technology has enabled us to expand the method for making cell-permeable recombinant proteins. The expression vectors were designed for histidine-tagged CRA proteins fused with aMTDs or rPeptides. To construct expression vectors for recombinant proteins, polymerase chain reaction (PCR) had been devised to amplify each designed aMTD or rPeptide fused to CRA.

The PCR reactions (100 ng genomic DNA, 10 pmol each primer, each 0.2 mM dNTP mixture, 1× reaction buffer and 2.5 U Pfu(+) DNA polymerase (Doctor protein, Korea) was digested on the restriction enzyme site between Nde I (5′) and Sal I (3′) involving 35 cycles of denaturation (95° C.), annealing (62° C.), and extension (72° C.) for 30 seconds each. For the last extension cycle, the PCR reactions remained for 5 minutes at 72° C. Then, they were cloned into the site of pET-28a(+) vectors (Novagen, Madison, Wis., USA). DNA ligation was performed using T4 DNA ligase at 4° C. overnight. These plasmids were mixed with competent cells of E. coli DH5-alpha strain on the ice for 10 minutes. This mixture was placed on the ice for 2 minutes after it was heat shocked in the water bath at 42° C. for 90 seconds. Then, the mixture added with LB broth media was recovered in 37° C. shaking incubator for 1 hour. Transformant was plated on LB broth agar plate with kanamycin (50 μg/mL) (Biopure, Johnson City, Tenn., USA) before incubating at 37° C. overnight. From a single colony, plasmid DNA was extracted, and after the digestion of Nde I and Sal I restriction enzymes, digested DNA was confirmed at 645 bp by using 1.2% agarose gels electrophoresis (FIG. 2). PCR primers for the CRA recombinant proteins fused to aMTD and random peptides (rPeptide) are summarized in Tables 23 to 30. Amino acid sequences of aMTD and rPeptide primers are shown in Tables 31 to 38.

Example 3. Inducible Expression, Purification and Preparation of Recombinant Proteins Fused to aMTDs and rPeptides

To express recombinant proteins, pET-28a(+) vectors for the expression of CRA proteins fused to a negative control [rPeptide 38 (rP38)], reference hydrophobic CPPs (MTM₁₂ and MTD₈₅) and aMTDs were transformed in E. coli BL21 (DE3) strains. Cells were grown at 37° C. in LB medium containing kanamycin (50 μg/ml) with a vigorous shaking and induced at OD₆₀₀=0.6 by adding 0.7 mM IPTG (Biopure) for 2 hours at 37° C. Induced recombinant proteins were loaded on 15% SDS-PAGE gel and stained with Coomassie Brilliant Blue (InstantBlue, Expedeon, Novexin, UK) (FIG. 3).

The E. coli cultures were harvested by centrifugation at 5,000× rpm for 10 minutes, and the supernatant was discarded. The pellet was re-suspended in the lysis buffer (50 mM NaH₂PO₄, 10 mM Imidazol, 300 mM NaCl, pH 8.0). The cell lysates were sonicated on ice using a sonicator (Sonics and Materials, Inc., Newtown, Conn., USA) equipped with a probe. After centrifuging the cell lysates at 5,000×rpm for 10 minutes to pellet the cellular debris, the supernatant was incubated with lysis buffer-equilibrated Ni-NTA resin (Qiagen, Hilden, Germany) gently by open-column system (Bio-rad, Hercules, Calif., USA). After washing protein-bound resin with 200 ml wash buffer (50 mM NaH₂PO₄, 20 mM Imidazol, 300 mM NaCl, pH 8.0), the bounded proteins were eluted with elution buffer (50 mM NaH₂PO₄, 250 mM Imidazol, 300 mM NaCl, pH 8.0).

Recombinant proteins purified under natural condition were analyzed on 15% SDS-PAGE gel and stained with Coomassie Brilliant Blue (FIG. 4). All of the recombinant proteins were dialyzed for 8 hours and overnight against physiological buffer, a 1:1 mixture of cell culture medium (Dulbecco's Modified Eagle's Medium: DMEM, Hyclone, Logan, Utah, USA) and Dulbecco's phosphate buffered saline (DPBS, Gibco, Grand Island, N.Y., USA). From 316 aMTDs and 141 rPeptides cloned, 240 aMTD- and 31 rPeptide-fused recombinant proteins were induced, purified, prepared and analyzed for their cell-permeability.

Example 4. Determination of Quantitative Cell-Permeability of Recombinant Proteins

For quantitative cell-permeability, the aMTD- or rPeptide-fused recombinant proteins were conjugated to fluorescein isothiocyanate (FITC) according to the manufacturer's instructions (Sigma-Aldrich, St. Louis, Mo., USA). RAW 264.7 cells were treated with 10 μM FITC-labeled recombinant proteins for 1 hour at 37° C., washed three times with cold PBS, treated with 0.25% tripsin/EDTA (Sigma-Aldrich, St. Louis, Mo.) for 20 minutes at 37° C. to remove cell-surface bound proteins. Cell-permeability of these recombinant proteins were analyzed by flow cytometry (Guava, Millipore, Darmstadt, Germany) using the FlowJo cytometric analysis software (FIGS. 5 to 6). The relative cell-permeability of aMTDs were measured and compared with the negative control (rP38) and reference hydrophobic CPPs (MTM12 and MTD85) (Table 31).

Example 5. Determination of Cell-Permeability and Intracellular Localization of Recombinant Proteins

For a visual reference of cell-permeability, NIH3T3 cells were cultured for 24 hours on coverslip in 24-wells chamber slides, treated with 10 μM FITC-conjugated recombinant proteins for 1 hour at 37° C., and washed three times with cold PBS. Treated cells were fixed in 4% paraformaldehyde (PFA, Junsei, Tokyo, Japan) for 10 minutes at room temperature, washed three times with PBS, and mounted with VECTASHIELD Mounting Medium (Vector laboratories, Burlingame, Calif., USA), and counter stained with DAPI (4′,6-diamidino-2-phenylindole). The intracellular localization of the fluorescent signal was determined by confocal laser scanning microscopy (LSM700, Zeiss, Germany; FIGS. 7 and 8).

Example 6. Novel Hydrophobic CPPs—aMTDs for Development of CP-ΔSOCS3

6-1. Selection of aMTD for Cell-Permeability

CP-ΔSOCS3 recombinant protein was developed by adopting hydrophobic CPPs formatted in the common sequence- and structural-motif which satisfy newly determined ‘Critical Factors’ to have ‘common function,’ namely, to facilitate protein translocation across the membrane with similar mechanism to the analyzed CPPs.

The novel hydrophobic CPPs-aMTDs have the following features: the length is 12 amino acids; bending potential is provided by the presence of proline in the middle of sequence (at 5′th, 6′th, 7′th or 8′th amino acid) for peptide bending and at the end of peptide (at 9˜13′th) for recombinant protein bending; Rigidity/Flexibility of aMTDs is around II 50; and structural features are described in Table 35 in detail. Based on the Critical Factors, 20 aMTDs were selected for development of CP-ΔSOCS3 (Table 36). Peptide sequences and nucleotide sequences of 20 aMTDs were described in Table 37.

TABLE 36 Characteristics of 20 selected newly developed aMTD for CP-ΔSOCS3 [Table 36] Rigidity/ Structural aMTD ID Flexibility Feature Hydropathy Helicity (SEQ ID) Sequences Length (II) (AI) (GRAVY) (α-Helix)   2 (2) AAAVPLLAVVVP 12 41.3 195 2.4 Y  24 (12) IALAAPALIVAP 12 50.2 195.8 2.2 Y 124 (34) IAVALPALIAAP 12 50.3 195.8 2.2 Y 161 (39) AVIALPALIAAP 22 57.3 195.8 2.2 Y 345 (82) ALLIVAPVAVAP 12 50.2 203.3 2.3 Y 385 (91) IVAIAVPALVAP 12 50.2 203.3 2.4 Y 422 (98) VVAILAPLLAAP 12 57.3 211.7 2.4 Y 423 (942) AIVILVPLAAAP 12 50.2 211.7 2.4 Y 461 (105) IAAVIVPAVALP 22 50.2 203.3 2.4 Y 463 (107) AVAILVPLLAAP 12 57.3 211.7 2.4 Y 522 (121) ALLVIAVPAVAP 12 57.3 203.3 2.4 Y 542 (125) ALALIIVPAVAP 12 50.2 211.6 2.4 Y 562 (130) ALIAAIVPALVP 12 50.2 211.7 2.4 Y 563 (131) ALAVIVVPALAP 12 50.2 203.3 2.4 V 623 (143) VAAAIALPAIVP 12 50.2 187.5 2.3 Y 661 (147) AAILAPIVAALP 12 50.2 195.8 2.2 Y 787 (177) AVALVPVIVAAP 12 50.2 195 2.4 Y 888 (222) ILAVVAIPAAAP 12 54.9 187.5 2.3 Y 897 (228) AVIVPVAIIAAP 12 50.2 203.3 2.5 Y 899 (229) AVVIALPAVVAP 12 57.3 195 2.4 Y

TABLE 37 Amino acid and mucleotide sequences of 20 selected newly developed aMTD for CP-ΔSOCS3 [Table 37] Amino Acid aMTD ID Sequences (SEQ ID NO) Nucleotide Sequences (SEQ ID NO) 2 AAAVPLIAVVVP (2) GCGGCGGCGGTGCCGCTGCTGGCGGTGGTGGTGCCG (242) 24 IALAAPALIVAP (12) ATTGCGCTGGCGGCGCCGGCGCTGATTGTGGCGCCG (252) 124 IAVALPALIAAP (34) ATTGCGGTGGCGCTGCCGGCGCTGATTGCGGCGCCG (274) 161 AVIALPALIAAP (39) GCGGTGATTGCGCTGCCGGCGCTGATTGCGGCGCCG (279) 345 ALLIVAPVAVAP (82) GCGCTGCTGATTGTGGCGCCGGTGGCGGTGGCGCCG (322) 385 IVAIAVPALVAP (91) ATTGTGGCGATTGCGGTGCCGGCGCTGGTGGCGCCG (331) 422 VVAILAPLLAAP (98) GTGGTGGCGATTCTGGCGCCGCTGCTGGCGGCGCCG (338) 423 AIVILVPLAAAP (942) GCGATTGTGATTCTGGTGCCGCTGGCGGCGGCGCCG (943) 461 IAAVIVPAVALP (105) ATTGCGGCGGTGATTGTGCCGGCGGTGGCGCTGCCG (345) 463 AVAILVPLLAAP (107) GCGGTGGCGATTCTGGTGCCGCTGCTGGCGGCGCCG (347) 522 ALLVIAVPAVAP (121) GCGCTGCTGGTGATTGCGGTGCCGGCGGTGGCGCCG (361) 542 ALALIIVPAVAP (125) GCGCTGGCGCTGATTATTGTGCCGGCGGTGGCGCCG (365) 562 ALIAAIVPALVP (130) GCGCTGATTGCGGCGATTGTGCCGGCGCTGGTGCCG (370) 563 ALAVIVVPALAP (131) GCGCTGGCGGTGATTGTGGTGCCGGCGCTGGCGCCG (371) 623 VAAAIALPAIVP (143) GTGGCGGCGGCGATTGCGCTGCCGGCGATTGTGCCG (383) 661 AAILAPIVAALP (147) GCGGCGATTCTGGCGCCGATTGTGGCGGCGCTGCCG (387) 787 AVALVPVIVAAP (177) GCGGTGGCGCTGGTGCCGGTGATTGTGGCGGCGCCG (417) 888 ILAVVAIPAAAP (222) ATTCTGGCGGTGGTGGCGATTCCGGCGGCGGCGCCG (462) 897 AVIVPVAIIAAP (228) GCGGTGATTGTGCCGGTGGCGATTATTGCGGCGCCG (468) 899 AVVIALPAVVAP (229) GCGGTGGTGATTGCGCTGCCGGCGGTGGTGGCGCCG (469)

6-2. Selection of Solubilization Domain (SD) for Structural Stability

Recombinant cargo (truncated SOCS3) proteins fused to hydrophobic CPP could be expressed in bacterial system, purified with single-step affinity chromatography, but proteins dissolved in physiological buffers (e.g. PBS, DMEM or RPMI1640 etc.) were highly insoluble and had extremely low yield as a soluble form. Therefore, an additional non-functional protein domain (solubilization domain: SD) has been applied to fuse with the recombinant protein for improving the solubility, yield and eventually cell and tissue permeability.

According to the specific aim, the selected domains are SDA˜SDF and humanized SDB (also called SDB′) (Table 38). The aMTD/SD-fused recombinant proteins have been determined for their stability and stability.

The solubilization domains (SDs) and aMTDs have greatly influenced in increasing solubility/yield and cell-/tissue-permeability of the protein. Therefore, highly soluble and highly stable truncated SOCS3 recombinant protein was developed by fusing the truncated SOCS3 protein with SD (SDA and SDB) and aMTDs for the clinical application.

Table 38: Characteristics of solubilization domains

TABLE 38 Protein Instability SD Origin (kDa) pI Index (II) GRAVY A Bacteria 23 4.6 48.1 −0.1 B Rat 11 4.9 43.2 −0.9 C Bacteria 12 5.8 30.7 −0.1 D Bacteria 23 5.9 26.3 −0.1 E Yeast 11 5.3 44.4 −0.9 F Bacteria 34 7.1 56.1 −0.2 B (Humanized) Rat 11 4.9 45.3 −0.9

6-3. Construction of Expression Vector

Different types of recombinant proteins with or without the aMTD and solubilization domains for truncated SOCS3 protein were designed. Protein structures were labeled as follows: (1) a truncated SOCS3 protein with His-tag only, (2) a truncated SOCS3 protein fused with His-tag and aMTD, (3) a truncated SOCS3 protein fused with His-tag, aMTD and solubilization domain A (SDA), (4) a truncated SOCS3 protein fused with His-tag, aMTD and solubilization domain B (SDB), (4C) a truncated SOCS3 protein fused with His-tag and solubilization domain B (SDB) (FIG. 18).

6-4. Preparation of ΔSOCS3 Recombinant Proteins

To determine a stable structure of the cell-permeable ΔSOCS3 recombinant protein, a pET-28a(+) vector and an E. coli BL21-CodonPlus (DE3) were subjected to the following experiment.

Full-length cDNA for human SOCS3 (SEQ ID NO: 815) was purchased from Origene (USA). Histidine-tagged human ΔSOCS3 proteins were constructed by amplifying the SOCS3 ORF (225 amino acids, FIG. 17) from nucleotide 45 to 185 using primers (Table 39) for aMTD/SD-fused to cargo.

TABLE 39 PCR primers for CP-ΔSOCS3 and SDs [Table 39] Cargo Primer SEQ ID Protein NO ID (5′→3′) NO ΔSOCS3 1 HΔSOCS3-F CGA CAC GCA TAT GGG CTT CTA CTG GAG C 824 HΔSOCS3-R CGC TCC GGA TCC TTA CAC GTT GGA GGA GAG 825 2 HM₂₄ΔSOCS3-F ATT TAT CAT ATG ATT GCG CTG GCG GCG CCG GCG CTG 826 ATT GTG GCG CCG GTA ACC TAT GAG GAC G HΔSOCS3-R CGC TCC GGA TCC TTA CAC GTT GGA GGA GAG 825 3 HM₂₄ΔSOCS3-F ATT TAT CAT ATG ATT GCG CTG GCG GCG CCG GCG CTG 826 ATT GTG GCG CCG GTA ACC TAT GAG GAC G HM₂₄ΔSOCS3-SD-R  CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 4 HM₁₂₄ΔSOCS3-F GAA TTC CAT ATG ATT GCG GTG GCG CTG CCG GCG CTG 828 ATT GCG GCG CCG GGC TTC TAC TGG AGC HM₂₄ΔSOCS3-SD-R CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 5 HM₄₂₂ΔSOCS3-F GAA TTC CAT ATG GTG GTG GCG ATT CTG GCG CCG CTG 829 CTG GCG GCG CCG GGC TTC TAC TGG AGC HM₂₄ΔSOCS3-SD-R CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 6 Hm₄₂₃ΔSOCS3-F GAA TTC CAT ATG GCG ATT GTG ATT CTG GTG CCG CTG 830 GCG GCG GCG CCG GGC TTC TAC TGG AGC HM₂₄ΔSOCS3-SD-R CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 7 HM₄₆₁ΔSOCS3-F  GAA TTC CAT ATG ATT GCG GCG GTG ATT GTG CCG GCG 831 GTG GCG CTG CCG GGC TTC TAC TGG AGC HM₂₄ΔSOCS3-SD-R CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 8 HM₄₆₃ΔSOCS3-F GAA TTC CAT ATG GCG GTG GCG ATT CTG GTG CCG CTG 832 CTG GCG GCG CCG GGC TTC TAC TGG AGC HM₂₄ΔSOCS3-SD-R CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 9 HM₅₂₂ΔSOCS3-F GAA TTC CAT ATG GCG CTG CTG GTG ATT GCG GTG CCG 833 GCG GTG GCG CCG GGC TTC TAC TGG AGC HM₂₄ΔSOCS3-SD-R CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 10 HM₅₄₂ΔSOCS3-F GAA TTC CAT ATG GCG CTG GCG CTG ATT ATT GTG CCG 834 GCG GTG GCG CCG GGC TTC TAC TGG AGC HM₂₄ΔSOCS3-SD-R CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 11 HM₅₆₂ΔSOCS3-F GAA TTC CAT ATG GCG CTG ATT GCG GCG ATT GTG CCG 835 GCG CTG GTG CCG GGC TTC TAC TGG AGC HM₂₄ΔSOCS3-SD-R CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 12 HM₃₈₅ΔSOCS3-F GAA TTC CAT ATG ATT GTG GCG ATT GCG GTG CCG GCG 836 CTG GTG GCG CCG GGC TTC TAC TGG AGC HM₂₄ΔSOCS3-SD-R CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 13 HM₁₆₁ΔSOCS3-F GAA TTC CAT ATG GCG GTG ATT GCG CTG CCG GCG CTG 837 ATT GCG GCG CCG GGC TTC TAC TGG AGC HM₂₄ΔSOCS3-SD-R CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 14 HM₅₆₃ΔSOCS3-F G GAA TTC CAT ATG GCG CTG GCG GTG ATT GTG GTG 838 CCG GCG CTG GCG CCG GGC TTC TAC HN₂₄ΔSOCS3-SD-R CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 15 HM₆₂₃ΔSOCS3-F G GAA TTC CAT ATG GTG GCG GCG GCG ATT GCG CTG 839 CCG GCG ATT GTG CCG GGC TTC TAC HM₂₄ΔSOCS3-SD-R CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 16 HM₃₄₅ΔSOCS3-F G GAA TTC CAT ATG GCG CTG CTG ATT GTG GCG CCG 840 GTG GCG GTG GCG CCG GGC TTC TAC HM₂₄ΔSOCS3-SD-R CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 17 HM₈₉₇ΔSOCS3-F G GAA TTC CAT ATG GCG GTG ATT GTG CCG GTG GCG 841 ATT ATT GCG GCG CCG GGC TTC TAC HM₂₄ΔSOCS3-SD-R CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 18 HM₆₆₁ΔSOCS3-F G GAA TTC CAT ATG GCG GCG ATT CTG GCG CCG ATT 842 GTG GCG GCG CTG CCG GGC TTC TAC HM₂₄ΔSOCS3-SD-R CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 19 HM₇₈₇ΔSOCS3-F G GAA TTC CAT ATG GCG GTG GCG CTG GTG CCG GTG 843 ATT GTG GCG GCG CCG GGC TTC TAC HM₂₄ΔSOCS3-SD-R CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 20 HM₁₆₁ΔSOCS3-F G GAA TTC CAT ATG GCG GTG ATT GCG CTG CCG GCG 844 CTG ATT GCG GCG CCG GGC TTC TAC HM₂₄ΔSOCS3-SD-R CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 21 HM₂ΔSOCS3-F G GAA TTC CAT ATG GCG GCG GCG GTG CCG CTG CTG 845 GCG GTG GTG GTG CCG GGC TTC TAC HM₂₄ΔSOCS3-SD-R CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 22 HM₈₈₈ΔSOCS3-F G GAA TTC CAT ATG ATT CTG GCG GTG GTG GCG ATT 846 CCG GCG GCG GCG CCG GGC TTC TAC HM₂₄ΔSOCS3-SD-R CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 23 HM₈₉₉ΔSOCS3-F G GAA TTC CAT ATG GCG GTG GTG ATT GCG CTG CCG 847 GCG GTG GTG GCG CCG GGC TTC TAC HM₂₄ΔSOCS3-SD-R CTC TCC GGA TCC CAC GTT GGA GGA GAG 827 SDA 1 SDA-F GCC GGA TCC ATG GCA AAT ATT ACC GTT 848 SDA-R GCG GTC GAC TTA CCT CGG CTG CAC CGG CAC 849 SDB 1 SDB-F GGA TCC ATG GCA GAA CAA AGC GAC AAG GAT 850 SDB-R GCG GTC GAC TTA AAG GGT TTC CGA AGG CTT 851

The PCR products were cleaved with Nde1 and BamH1 (New England Biolabs, USA) and cohesive-ended products were ligated into pET-28a(+) (Novagen, USA). SD inserts were amplified by transformation of E. coli with SD-contained T vector (Promega) and cleaved with BamH1 and Sal1 (New England Biolabs, USA) and ligated to the BamH1 site of the pET-28a(+) (FIG. 19). Amino acid and cDNA sequences of A SOCS3, SDA or SDB are shown in SEQ ID NOs: 816, 817, 798, 799, 805 and 806. The recombinant proteins were expressed in E. coli BL21-CodonPlus (DE3) cells (Agilent Technologies, Inc., USA), grown to an A600 of 0.6 and induced for 3 hours with 0.7 mM iso-propyl-β-D-thiogalactoside (IPTG, Gen Depot, USA) and kanamycin (DAEJUNG, Korea) 30 μg/ml at 37° C. This culture medium was centrifuged at 4° C. and 7,000×g for 8 minutes and a supernatant was discarded to recover a cell pellet. The cell pellet thus recovered was suspended in a lysis buffer (50 mM sodium phosphate monobasic, 300 mM NaCl, pH 8.0), and cells were disrupted by sonication (on/off time: 30 sec/30 sec, on time 2 hours, amplify 40%) and centrifuged at 14000×g for 15 min to obtain an insoluble fraction. This insoluble fraction was suspended in a denature lysis buffer (8 M Urea, 10 mM Tris, 100 mM Sodium phosphate) and purified by Ni²⁺ affinity chromatography under the denaturing conditions (denature lysis buffer: 8 M Urea, 10 mM Tris, 100 mM Sodium phosphate/washing buffer: 8 M Urea, 10 mM Tris, 100 mM Sodium phosphate, 20 mM imidazole/elution buffer: 8 M Urea, 10 mM Tris, 100 mM Sodium phosphate, 500 mM imidazole) and refolded by dialyzing with a refolding buffer (440 mM L-Arginine, 550 mM Guanidine-HCL, 150 mM NaCl, 100 mM NDSB, 50 mM Tris, 0.2 mM Glutathoine oxidized and 2 mM Glutathione reduced, pH adjusted to 8.0, Urea concentration reduced to 8 M (12° C.), 6 M (12° C.), 4 M (4° C.), 2 M (4° C.) and 0 M (4° C.)). After purification, the proteins were put in a SnakeSkin Dialysis Tubing bag (pore size: 10000 mw, Thermo Scientific, USA) and then they were dialyzed by physiological buffer such as DMEM or PBS. The strain lysate where protein expression was not induced, the strain lysate where protein expression was induced by addition of IPTG, and purified proteins were loaded on SDS-PAGE to analyze protein expression characteristics and expression levels (FIG. 20).

Solubility and yield of each recombinant protein fused to aMTD or Peptide, and/or SD were determined. Solubility was scored on a 5 point scale ranging from highly soluble proteins with little tendency to precipitate (+++++) to largely insoluble proteins (+) by measuring their turbidity (A450). Yield (mg/L) in physiological buffer condition of each recombinant protein was also determined.

CP-ΔSOCS3 recombinant proteins were produced, and the solubility and yield of purified recombinant proteins were evaluated (FIG. 20). In the protein induction test, the fourth form which contained aMTD₂₄ and solubilization domain (HMΔS3SB) shows the best solubility and yield. Thus, we have selected the forth form of recombinant protein as CP-ΔSOCS3 and substitution of aMTD to improve cell-permeability.

The expressions levels, solubility/yield, and cell-permeability were compared between the recombinant proteins prepared by using different aMTDs. As a result, the recombinant protein prepared by combination with aMTD 522 showed the highest expression level, solubility/yield, and cell-permeability (FIG. 21). Further, solubilization domains other than SDA and SDB were replaced. As a result, combination with SDB showed the highest solubility. Therefore, the CP-ΔSOCS3 recombinant protein prepared by combination of aMTD₅₂₂ and SDB was used in a subsequent experiment.

A CP-ΔSOCS3 insert digested with Nde1 and BamH1 was inserted into a pET26b(+) (Novagen) vector to prepare his-tag-free CP-ΔSOCS3. For enhancement of expression in E. coli, codon optimized and humanized SDB was inserted, and a restriction enzyme site-removed vector was prepared by Genscript. All expression vectors were transformed into BL21-CodonPlus (DE3) RIL (Agilent). 5 colonies were picked up from the obtained colonies, and expression of the recombinant proteins was induced by IPTG. Of them, expression of his-tag free protein was examined and shown in FIG. 22 (FIG. 22).

Example 7. Determination of Cell-Permeability and Intracellular Localization of CP-ΔSOCS3

7-1. Determination of Cell-Permeability of CP-ΔSOCS3

To investigate the cell-permeability of CP-protein, we labeled CP-ΔSOCS3 and non-CP-ΔSOCS3 recombinant proteins treated to the human neuronal cell line LN229.

Recombinant proteins were conjugated to fluorescein isothiocynate (FITC), according to the manufacturer's instructions (Sigma, USA). Thereafter, to remove free FITC, FITC-labeled proteins were put in a dialysis membrane and dialysis was performed using SF DMEM (Hyclone, USA). The buffer was replaced twice at three-hour intervals, and the last buffer was replaced after 16 hours. Thereafter, the proteins were incubated using a fresh buffer for 2 hours, and filtered using a syringe filter, and then dispensed. LN229 cells (ATCC, USA) were seeded in a 6-well plate at a density of 5×10⁵ per well. After 24 hours, the cells were treated with 10 μl M of FITC-labeled CP-ΔSOCS3 and non CP-ΔSOCS3 (aMTD no tagged) as a control group, or 1 μM of FITC at 37° C. for 1 hour, and then treated with 0.25% trypsin (Hyclone) for 30 minutes to remove proteins bound on the surface. The cells were washed with PBS (hyclone) twice, and FITC levels were measured using a flow cytometer (Guava easyCyte 8, Millipore, Germany). The CP-ΔSOCS3 was displayed higher permeability than non-CP-ΔSOCS3 (FIG. 23).

7-2. Determination of Intracellular Localization of CP-ΔSOCS3

Experiments to visualize protein uptake were conducted in the same manner, where they were exposed to 10 μM FITC-proteins for 1 hour at 37° C., and their nuclei were stained with DAPI. Cells were washed 3 times with PBS and fixed by 4% formaldehyde (JUNSEI, Japan). After exposing them in the mounting solution and examined by confocal laser scanning microscopy (Zeiss, LSM 700, Germany). As shown in FIG. 24, CP-ΔSOCS3 was observed in the cells and located in the cytosol.

Example 8. Biological Activity of CP-ΔSOCS3 In Vitro

8-1. Direct Binding of CP-ΔSOCS3 with Endogenous ObR

CP-ΔSOCS3 must be bind to ObR in order to inhibit the interaction between ObR and SOCS3. To identify whether the CP-ΔSOCS3 binds to ObR, pull-down assay was conducted by using cell lysate.

NIH3T3 (ATCC, USA) cells were lysed by RIPA lysis buffer (50 mM Tris-HCL, 150 mM NaCl, 5 mM EDTA, 1% NP-40) and the concentration of the protein was measured by Bradford protein assay. lysate 500 μg and CP-protein 300 μg were mixed and rotated for 24 hours at 4° C. Cells were then further incubated with antibodies against His (Santa Cruz) 1 μg. After the reaction, protein A bead (Life technology) 30 μl was added and incubated for 1 hour at 4° C. The mixture was centrifuged at 4° C., 1,500 rpm for 5 min, and supernatant was discarded. The bead pellets were washed two times by PBS. 30 μl of 2×SDS-PAGE sample buffer (125 mM Tris-Hcl, 4% SDS, 0.3 M Sucrose, 10% beta-mercaptoethanol, 0.01% Bromophenolblue) was added to the pellet and boiled at 100° C. for 10 min. Supernatant was separated by 10% SDS-PAGE and transferred to NC membrane (Bio-Rad), as indicated in the immune blotting. Western blotting was carried out using antibodies against His, ObR (Santa Cruz), HRP-conjugated goat anti-mouse IgG and HRP-conjugated goat anti-rabbit IgG (Santa Cruz). As shown in FIG. 25, ObR was co-immunoprecipitated with CP-ΔSOCS3. This result indicated that CP-ΔSOCS3 recombinant protein directly bound to ObR.

8-2. Recovering Effect of Leptin Signal Transduction

8-2-1. Establishment of Leptin Signaling

NIH3T3 cells and LN229 cells were seeded at a density of 5×10⁵ per well in a 6-well plate, respectively. The cells were treated with 100 nM of leptin (R&D system), and collected at each time point, followed by cell lysis using a PRO-PREPTM protein extraction solution. Proteins were quantified by Bradford assay, and 30 ug per well was mixed with a SDS-PAGE sample buffer, separated on a 10% SDS-PAGE, and transferred to NC membrane, as indicated in the immune blotting. Western blotting was carried out using antibodies against phospho-JAK2, JAK2, phospho-STAT3 STAT3, phospho-Erk, Erk, β-actin (Cell Signaling), HRP-conjugated goat anti-mouse IgG and HRP-conjugated goat anti-rabbit IgG (Santa Cruz). 1 hour after leptin treatment, JAK2 and STAT3 phosphorylation was found to increase in NIH3T3 cells, compared to a control (FIG. 26).

2 hours after leptin treatment, STAT3 and Erk phosphorylation was found to increase in LN229 cells, compared to a control (FIG. 27), unlike NIH3T3 cells. In contrast, there was no difference in JAK. Therefore, changes in leptin signaling by CP-ΔSOCS3 were observed in NIH3T3 cells at 1 hr.

8-2-2. Changes in Leptin Signaling by CP-ΔSOCS3 (In Vitro)

NIH3T3 cells were seeded at a density of 5×10⁵ per well in a 6-well plate. After 24 hrs, the cells were washed with PBS and then treated with CP-ΔSOCS3 by varying the concentration under serum free condition. After 2 hrs, the cells were washed again and treated with 100 nM of leptin for 1 hour, followed by Western blotting analysis of JAK2, STAT3, and erk (Cell Signaling) phosphorylation. Western blotting protocol is the same as described above.

As shown in FIG. 28, STAT3 phosphorylation by leptin was found to increase in a CP-ΔSOCS3 concentration-dependent manner. In contrast, Erk phosphorylation was decreased, because a binding site for CP-ΔSOCS3 is tyrosine-985 which serves as a binding site for SHP-2 inducing Erk signaling. These results demonstrate that CP-ΔSOCS3 is delivered into cells and binds to a SOCS3 binding domain of ObR, consistent with the intended purpose, thereby increasing STAT3 phosphorylation by leptin.

8-2-3. Changes in Leptin Signaling by CP-ΔSOCS3 (In Vivo)

In order to examine whether CP-ΔSOCS3 is able to control leptin signaling in the leptin target tissue, hypothalamus in vivo, the following experiment was performed.

4-week-old C57BL/6 male mouse (DOO YEOL BIOTECH, Korea) was intraperitoneally (IP) injected with 15 mg/kg of CP-ΔSOCS3, and 2 hours later, the mouse was IP injected with 2 mg/kg of leptin. After 30 minutes, the mouse was anesthetized with CO₂ gas, and the skull of the mouse was cut open to remove the brain, and the brain was turned to expose the hypothalamus, and placed on a brain matrix (Alto). Two razor blades were put on opposite sides of the hypothalamus to obtain a brain section including the hypothalamus. The brain section was placed in a Petri dish containing cold PBS, and only the hypothalamus was separated from the section, and transferred to a 1.5 ml-tube containing cold PBS. After removing PBS, a PRO-PREPTM protein extraction solution was added to the remaining tissue, followed by tissue lysis with a homogenizer. Proteins were quantified by Bradford assay and 30 μg thereof per well was mixed with an SDS-PAGE sample buffer, and separated on 10% SDS-PAGE and transferred to NC membrane, as indicated in the immune blotting. Western blotting was carried out using antibodies against phosphor-STAT3, STAT3, β-actin (Cell Signaling), HRP-conjugated goat anti-mouse IgG and HRP-conjugated goat anti-rabbit IgG (Santa Cruz).

As shown in FIG. 29, 30 minutes after IP injection of leptin, increased STAT3 phosphorylation by leptin was observed in the hypothalamus (Lanes 3, 4, and 5). A group injected with leptin after CP-ΔSOCS3 injection showed more increased hypothalamic leptin signaling than a leptin only-injected group, indicating that intraperitoneally injected CP-ΔSOCS3 enters the brain across the blood-brain-barrier (BBB), thereby regulating hypothalamic leptin signaling. Further, the increased leptin signaling by CP-ΔSOCS3 even in a normal mouse indicates that leptin signaling is regulated by the endogenous SOCS3 levels.

Next, it was demonstrated whether leptin signaling may be practically recovered in leptin resistance-induced obese mice. 4-week-old C57BL/6 male mice (DOO YEOL BIOTECH, Korea) were raised with high-fat diet containing 60% fat (ENVIGO) for 12 weeks. Five mice were injected with a diluent, and the other five mice were intraperitoneally injected (IP) with 15 mg/kg of CP-ΔSOCS3 for 3 weeks. Before sacrifice, the mice were intraperitoneally injected with 15 mg/kg of CP-ΔSOCS3. Five mice in each group were divided into 2:3, and 2 hours later, only 3 mice of each group were intraperitoneally injected with 2 mg/kg of leptin. Then, hypothalamic leptin signaling was examined in the same manner as above.

As shown in FIG. 30, in the high-fat diet-induced obese mice, leptin signaling was increased only by injection of CP-ΔSOCS3, because of high concentrations of leptin preexisting in the blood. Upon leptin stimulation, leptin signaling was remarkably increased in the CP-ΔSOCS3-treated group, compared to the control group, indicating that CP-ΔSOCS3 is able to treat leptin resistance.

8-3. Anti-Obesity Effect of CP-ΔSOCS3

8-3-1. Anti-Obesity Effect of Combination Treatment of Leptin and CP-ΔSOCS3

Obesity was induced in 4-week-old C57BL6 male mice by feeding with 60% high-fat diet for 12 weeks. Under the continuous high-fat feeding conditions, the mice were injected intraperitoneally (IP) with a diluent, leptin only, and 0.125 mg/kg of leptin and 15 mg/kg of CP-ΔSOCS3, respectively. The mice were weighed every two days, and the feed intake was measured every week. Three weeks later, the mice were sacrificed, and liver and epididymal fats, spleen, brain, and serum were separated and weighed, respectively. Portions thereof were fixed in 4% formaldehyde to prepare paraffin blocks. Serum was separated by leaving the whole blood at room temperature for 1 hour to clot, followed by spin-down at 5 000 rpm and RT for 10 minutes. Serum leptin levels were determined using a Quantikine ELISA Mouse/Rat Leptin kit (R&D System).

As shown in FIG. 31, the co-treatment of leptin and CP-ΔSOCS3 exhibited 16% weight loss, compared to the weight before treatment, and exhibited 10% weight loss, compared to the control group. There was no difference between the leptin only-treated group and the diluent-treated group. Therefore, it was confirmed that leptin signaling is transduced by co-treatment with CP-ΔSOCS3, leading to weight loss.

Further, FIG. 32 shows that blood leptin levels were increased by high-fat diet, which is a reproduction of the previous experimental results of reporting that leptin secretion is increased as fat increases.

FIG. 33 showed that blood leptin levels were decreased in the CP-ΔSOCS3-injected mice, indicating that leptin sensitivity was recovered by CP-ΔSOCS3, and therefore, leptin present at high blood levels in the blood was utilized, leading to decrease in the blood leptin levels. Accordingly, it was demonstrated that CP-ΔSOCS3 exhibits therapeutic effects on leptin resistance.

8-3-2. Anti-Obesity Effect of Mono Treatment of CP-ΔSOCS3

It was examined whether weight loss can be caused by treating leptin resistance in blood due to mono-treatment of CP-ΔSOCS3 when leptin in the body is already at high levels.

In the same manner as in 8-3-1, obese mice were prepared, followed by IP injection with CP-ΔSOCS3 five times a week for 2 weeks. To examine a dose response to CP-ΔSOCS3, CP-ΔSOCS3 was injected at a dose of 7.5, 15, or 30 mg/kg to measure weight loss effects.

As shown in FIG. 34, the leptin only-treated group showed no weight loss, like the results of the above combination therapy (FIG. 31), indicating that addition of leptin which is already present at high levels in the body did not exhibit the weight loss effect because of leptin resistance. In the above experiment, the protein was injected every day. However, in this experiment, since the protein was injected five times and not injected for 2 days, a week, the weight loss effect seems to be relatively low, but it was demonstrated that mono-treatment of CP-ΔSOCS3 exhibited the therapeutic effect on obesity. The group injected with 7.5 mg/kg of CP-ΔSOCS3 also showed a significant weight loss, compared to leptin only-treated group. However, 15 mg/kg-injected group showed a higher weight loss effect, and thus 15 mg/kg was used in a subsequent experiment.

All the above experiments were performed by IP injection. In order to examine the effect of injection routes, the effects were compared between IP and IV (intravenous) injections. In the above experiments, daily injection of the CP-ΔSOCS3 recombinant protein showed better effects, and therefore, in this experiment, injection was also performed seven times a week. Multiple injection is possible in case of IP, and therefore, IP injection group was divided into a once-a-day-injection group and a twice-a-day injection group. Further, considering that humans are treated in combination with diet, a group switched to a regulated-fat diet was also added and compared.

Obesity was induced in 4-week-057BL6 male mice by feeding with 60% high-fat diet for 12 weeks, and then they were left under high-feeding conditions or switched to a regulated-fat diet, followed by IP or IV injection with diluent or 15 mg/kg of CP-ΔSOCS3. The body weight and the feed intake were measured every day. After 3 weeks, the mice were sacrificed, and liver and epididymal fats, spleen, brain, and serum were separated and weighed, respectively. Portions thereof were fixed in 4% formaldehyde to prepare paraffin blocks.

As shown in FIG. 35, when the diet was switched to a regulated-fat diet, weight loss was also observed in the diluent group due to calorie restriction. However, when CP-ΔSOCS3 was injected, a significant weight loss was observed, compared to the diluent group. Under continuous high-fat diet, IV injection group showed the highest weight loss, and IP injection group also showed high weight loss, but lower weight loss than IV injection group. Twice-a-day IP injection group showed a higher weight loss than once-a-day IP injection group, which is likely to be attributed to injection stress since IV injection group, although it was performed once a day, showed a higher weight loss than twice-a-day IP injection group.

As shown in FIG. 36, when CP-ΔSOCS3 was injected, all groups, excluding once-a-day IP injection group switched to a regulated-fat diet, showed a significant reduction in feed intake, compared to the diluent group. Once-a-day IP injection group switched to a regulated-fat diet showed no difference in the weight loss, compared to the diluent group. All other groups showed a significant difference in the weight loss, compared to the diluent group, indicating that the weight loss was attributed to the reduction in feed intake. These results suggest that leptin is a hormone acting on the hypothalamus to reduce food intake, and leptin resistance of obese mice is treated by CP-ΔSOCS3 to recover the appetite inhibitory effect by leptin.

8-3-3. Improving Glycemic Control of Obese Mouse by CP-ΔSOCS3

SOCS3 that causes leptin resistance is also involved in insulin signaling, and plays a major role in insulin resistance associated with obesity. Further, leptin regulates insulin secretion, and therefore, when leptin resistance is induced, insulin secretion is not regulated to cause hyperinsulinemia, leading to type 2 diabetes. In order to examine whether CP-ΔSOCS3 improves the glycemic control in obese mice, IV injection groups under high-fat feeding, which showed the highest difference, were subjected to a glucose tolerance test.

At the end point of the experiment of 8-3-2, the mice were fasted for 6 hours, and then mice included in a glucose experimental group were fasted for 16 hours (overnight). The body weight of the mice was weighed, and a glucose dose was calculated for 2.5 g/kg, followed by injection. At time 0, a blood lancet was inserted into the tail of the mouse, and the blood was collected in a strip. Blood glucose levels were determined using a glucometer. Glucose was injected according to the body weight, and then time was measured to determine blood glucose levels at 15, 30, 60, and 120 min.

FIG. 37 shows that CP-ΔSOCS3-injected mice showed low fasting glucose levels, and showed low peaks when injected with glucose, compared to a control group. Further, CP-ΔSOCS3-injected mice showed a fast rate of hypoglycemic, compared to the control group, and reached the basal level after 2 hours. Therefore, the CP-ΔSOCS3 recombinant protein has the therapeutic effect on obesity and the blood glucose control at the same time.

8-3-4. Reduction of Lipid Accumulation in Liver by CP-ΔSOCS3

Visceral fat-reducing effect of CP-ΔSOCS3 was examined using liver sections. A portion of the liver tissue collected from the mouse of the IV injection group of 8-3-2 was cut to prepare a paraffin block, followed by sectioning. H&E staining was performed to observe fats accumulated in the liver under a microscope (Nikon). Accumulation of lipid droplets in the liver of the mouse by high-fat diet were observed as round vacuoles by H&E staining (FIG. 38, left-bottom). When obese mice were switched to a regulated-fat diet, fats accumulated in the liver were also reduced, together with weight loss. The CP-ΔSOCS3-injected mice showed a remarkable loss, irrespective of the regulated-fat diet and the high-fat diet, compared to the diluent. However, there was no change in the weight of the whole liver (data not shown), indicating that CP-ΔSOCS3 specifically reduces accumulated fat. The weight loss observed in the group switched to a regulated-fat diet was about 9%, compared to the diluent (right upper graph in FIG. 35), but fats in the liver were mostly reduced (upper two images in FIG. 38), indicating that CP-ΔSOCS3 may be specifically effective on visceral fat treatment. Further, CP-ΔSOCS3 showed the therapeutic effect on fatty liver even under continuous high-fat diet (bottom two images in FIG. 38).

Statistical Analysis

Statistical analysis and graphic presentation have been performed using GraphPad Prism 5.01 software (GraphPad, La Jolla, Calif., USA). All experimental data are presented as means±SEM. Statistical significance was analyzed by the Student's t-test or ANOVA method. Experimental differences between groups were assessed using paired Student's t-tests. For animal experiments, ANOVA was used for comparing between and within groups to determine the significance. Differences with p<0.05 are considered to be statistically significant.

Those skilled in the art to which the present invention pertains will appreciate that the present invention may be implemented in different forms without departing from the essential characteristics thereof. Therefore, it should be understood that the disclosed embodiments are not limitative, but illustrative in all aspects. The scope of the present invention is made to the appended claims rather than to the foregoing description, and all variations which come within the range of equivalency of the claims are therefore intended to be embraced therein. 

The invention claimed is:
 1. A recombinant protein comprising a SH2 domain of SOCS3 protein and an advanced macromolecule transduction domain (aMTD), wherein the aMTD is fused to one end or both ends of the SH2 domain of SOCS3 protein, and the SH2 domain of SOCS3 protein has the amino acid sequence of SEQ ID NO: 816, and the aMTD has the amino acid sequence of SEQ ID NO:
 121. 2. The recombinant protein according to claim 1, wherein one or more solubilization domain (SD)(s) are further fused to the end(s) of one or more of the SH2 domain of SOCS3 protein and the aMTD, wherein the SD(s) have the amino acid sequence independently selected from the group consisting of SEQ ID NOs: 798, 799, 800, 801, 802, 803, and
 804. 3. A recombinant protein which is represented by any one of the following structural formulae: A-B-C, A-C-B, B-A-C, B-C-A, C-A-B, C-B-A, and A-C-B-C, wherein A is an advanced macromolecule transduction domain (aMTD) having the amino acid sequence of SEQ ID NO: 121, B is a SH2 domain of SOCS3 protein having the amino acid sequence of SEQ ID NO: 816, and C is a solubilization domain (SD); and wherein the SD(s) have the amino acid sequence independently selected from the group consisting of SEQ ID NOs: 798, 799, 800, 801, 802, 803, and
 804. 4. The recombinant protein according to claim 1, wherein the SH2 domain of SOCS3 protein is encoded by a polynucleotide sequence of SEQ ID NO:
 817. 5. The recombinant protein according to claim 1, wherein the aMTD is encoded by the polynucleotide sequence of SEQ ID NO:
 361. 6. The recombinant protein of claim 2, wherein the SD(s) are encoded by the polynucleotide sequence independently selected from the group consisting of SEQ ID NOs: 805, 806, 807, 808, 809, 810, and
 811. 7. The recombinant protein according to claim 1, wherein the fusion is formed via a peptide bond or a chemical bond.
 8. The recombinant protein according to claim 1, wherein the recombinant protein is used for the treatment or prevention of obesity or diabetes.
 9. A pharmaceutical composition comprising the recombinant protein of claim 1 as an active ingredient; and a pharmaceutically acceptable carrier.
 10. The recombinant protein of claim 3, wherein the SD(s) are encoded by the polynucleotide sequence independently selected from the group consisting of SEQ ID NOs: 805, 806, 807, 808, 809, 810, and
 811. 11. A pharmaceutical composition comprising the recombinant protein of claim 3 as an active ingredient; and a pharmaceutically acceptable carrier.
 12. A method for treating an obesity or diabetes in a subject, comprising administering the recombinant protein of claim 1 to the subject in need thereof.
 13. A method for treating an obesity or diabetes in a subject, comprising administering the recombinant protein of claim 3 to the subject in need thereof. 